bismark: bismark_deduplicate/deduplicate

annotate bismark_deduplicate/deduplicate_bismark @ 24:b2b75548b4eb draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'

author	bgruening
date	Sat, 06 May 2017 13:12:54 -0400
parents
children

rev	line source
24 b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1 #!/usr/bin/env perl
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	2 use strict;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	3 use warnings;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	4 use Getopt::Long;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	5
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	6
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	7 ### This script is supposed to remove alignments to the same position in the genome which can arise by e.g. PCR amplification
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	8 ### Paired-end alignments are considered a duplicate if both partner reasd start and end at the exact same position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	9
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	10 ### May 13, 2013
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	11 ### Changed the single-end trimming behavior so that only the start coordinate will be used. This avoids duplicate reads that have been trimmed to a varying extent
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	12 ### Changed the way of determining the end of reads in SAM format to using the CIGAR string if the read contains InDels
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	13
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	14 ### 16 July 2013
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	15 ### Adding a new deduplication mode for barcoded RRBS-Seq
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	16
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	17 ### 27 Sept 2013
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	18 ### Added close statement for all output filehandles (which should probably have been there from the start...)
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	19
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	20 ### 8 Jan 2015
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	21 ### to detect paired-end command from the @PG line we are no requiring spaces before and after the -1 or -2
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	22
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	23 ### 09 Mar 2015
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	24 ### Removing newline characters also from the read conversion flag in case the tags had been reordered and are now present in the very last column
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	25
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	26 ### 19 08 2015
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	27 ### Hiding the option --representative from view to discourage people from using it (it was nearly always not what they wanted to do anyway). It should still work
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	28 ### for alignments that do not contain any indels
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	29 ### Just for reference, here is the the text:
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	30 ### print "--representative\twill browse through all sequences and print out the sequence with the most representative (as in most frequent) methylation call for any given position. Note that this is very likely the most highly amplified PCR product for a given sequence\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	31
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	32
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	33 my $dedup_version = 'v0.16.3';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	34
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	35 my $help;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	36 my $representative;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	37 my $single;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	38 my $paired;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	39 my $global_single;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	40 my $global_paired;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	41 my $vanilla;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	42 my $samtools_path;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	43 my $bam;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	44 my $rrbs;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	45 my $version;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	46
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	47 my $command_line = GetOptions ('help' => \$help,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	48 'representative' => \$representative,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	49 's\|single' => \$global_single,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	50 'p\|paired' => \$global_paired,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	51 'vanilla' => \$vanilla,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	52 'samtools_path=s' => \$samtools_path,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	53 'bam' => \$bam,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	54 'barcode' => \$rrbs,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	55 'version' => \$version,
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	56 );
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	57
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	58 die "Please respecify command line options\n\n" unless ($command_line);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	59
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	60 if ($help){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	61 print_helpfile();
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	62 exit;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	63 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	64
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	65 if ($version){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	66 print << "VERSION";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	67
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	68 Bismark Deduplication Module
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	69
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	70 Deduplicator Version: $dedup_version
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	71 Copyright 2010-16 Felix Krueger, Babraham Bioinformatics
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	72 www.bioinformatics.babraham.ac.uk/projects/bismark/
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	73
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	74
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	75 VERSION
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	76 exit;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	77 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	78
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	79
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	80
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	81 my @filenames = @ARGV;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	82
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	83 unless (@filenames){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	84 print "Please provide one or more Bismark output files for deduplication\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	85 sleep (2);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	86 print_helpfile();
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	87 exit;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	88 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	89
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	90
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	91 ### OPTIONS
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	92 unless ($global_single or $global_paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	93 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	94 die "Please specify either -s (single-end) or -p (paired-end) for deduplication. Reading this information from the \@PG header line only works for SAM/BAM files\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	95 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	96 warn "\nNeither -s (single-end) nor -p (paired-end) selected for deduplication. Trying to extract this information for each file separately from the \@PG line of the SAM/BAM file\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	97 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	98
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	99 if ($global_paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	100 if ($global_single){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	101 die "Please select either -s for single-end files or -p for paired-end files, but not both at the same time!\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	102 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	103 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	104
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	105 if ($rrbs){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	106 die "Barcode deduplication only works with Bismark SAM (or BAM) output (in attempt to phase out the vanilla format)\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	107 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	108
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	109 warn "Processing paired-end custom Bismark output file(s):\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	110 warn join ("\t",@filenames),"\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	111 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	112 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	113 warn "Processing paired-end Bismark output file(s) (SAM format):\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	114 warn join ("\t",@filenames),"\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	115 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	116 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	117 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	118 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	119 warn "Processing single-end custom Bismark output file(s):\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	120 warn join ("\t",@filenames),"\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	121 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	122 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	123 warn "Processing single-end Bismark output file(s) (SAM format):\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	124 warn join ("\t",@filenames),"\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	125 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	126 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	127
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	128 ### PATH TO SAMTOOLS
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	129 if (defined $samtools_path){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	130 # if Samtools was specified as full command
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	131 if ($samtools_path =~ /samtools$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	132 if (-e $samtools_path){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	133 # Samtools executable found
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	134 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	135 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	136 die "Could not find an installation of Samtools at the location $samtools_path. Please respecify\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	137 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	138 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	139 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	140 unless ($samtools_path =~ /\/$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	141 $samtools_path =~ s/$/\//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	142 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	143 $samtools_path .= 'samtools';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	144 if (-e $samtools_path){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	145 # Samtools executable found
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	146 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	147 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	148 die "Could not find an installation of Samtools at the location $samtools_path. Please respecify\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	149 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	150 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	151 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	152 # Check whether Samtools is in the PATH if no path was supplied by the user
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	153 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	154 if (!system "which samtools >/dev/null 2>&1"){ # STDOUT is binned, STDERR is redirected to STDOUT. Returns 0 if Samtools is in the PATH
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	155 $samtools_path = `which samtools`;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	156 chomp $samtools_path;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	157 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	158 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	159
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	160 if ($bam){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	161 if (defined $samtools_path){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	162 $bam = 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	163 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	164 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	165 warn "No Samtools found on your system, writing out a gzipped SAM file instead\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	166 $bam = 2;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	167 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	168 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	169 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	170 $bam = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	171 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	172
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	173
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	174 if ($representative){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	175 warn "\nIf there are several alignments to a single position in the genome the alignment with the most representative methylation call will be chosen (this might be the most highly amplified PCR product...)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	176 sleep (1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	177 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	178 elsif($rrbs){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	179 warn "\nIf the input is a multiplexed sample with several alignments to a single position in the genome, only alignments with a unique barcode will be chosen)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	180 sleep (1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	181 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	182 else{ # default; random (=first) alignment
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	183 warn "\nIf there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	184 sleep (1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	185 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	186
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	187 foreach my $file (@filenames){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	188
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	189 if ($global_single){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	190 $paired = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	191 $single = 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	192 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	193 elsif($global_paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	194 $paired = 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	195 $single = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	196 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	197
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	198 unless($global_single or $global_paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	199
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	200 warn "Trying to determine the type of mapping from the SAM header line\n"; sleep(1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	201
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	202 ### if the user did not specify whether the alignment file was single-end or paired-end we are trying to get this information from the @PG header line in the SAM/BAM file
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	203 if ($file =~ /\.gz$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	204 open (DETERMINE,"gunzip -c $file \|") or die "Unable to read from gzipped file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	205 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	206 elsif ($file =~ /\.bam$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	207 open (DETERMINE,"$samtools_path view -h $file \|") or die "Unable to read from BAM file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	208 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	209 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	210 open (DETERMINE,$file) or die "Unable to read from $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	211 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	212 while (<DETERMINE>){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	213 last unless (/^\@/);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	214 if ($_ =~ /^\@PG/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	215 # warn "found the \@PG line:\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	216 # warn "$_";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	217
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	218 if ($_ =~ /\s+-1\s+/ and $_ =~ /\s+-2\s+/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	219 warn "Treating file as paired-end data (extracted from \@PG line)\n"; sleep(1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	220 $paired = 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	221 $single = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	222 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	223 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	224 warn "Treating file as single-end data (extracted from \@PG line)\n"; sleep(1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	225 $paired = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	226 $single = 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	227 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	228 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	229 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	230 close DETERMINE or warn "$!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	231 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	232
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	233 if ($file =~ /(\.bam$\|\.sam$)/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	234 bam_isEmpty($file);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	235 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	236
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	237
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	238 ### OPTIONS
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	239 unless ($single or $paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	240 die "Please specify either -s (single-end) or -p (paired-end) for deduplication, or provide a SAM/BAM file that contains the \@PG header line\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	241 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	242
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	243 ###
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	244 unless ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	245 if ($paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	246 test_positional_sorting($file);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	247 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	248 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	249
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	250
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	251 ### writing to a report file
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	252 my $report = $file;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	253
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	254 $report =~ s/\.gz$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	255 $report =~ s/\.sam$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	256 $report =~ s/\.bam$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	257 $report =~ s/\.txt$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	258 $report =~ s/$/.deduplication_report.txt/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	259
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	260 open (REPORT,'>',$report) or die "Failed to write to report file to $report: $!\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	261
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	262
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	263 ### for representative methylation calls we need to discriminate between single-end and paired-end files as the latter have 2 methylation call strings
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	264 if($representative){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	265 deduplicate_representative($file);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	266 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	267
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	268 elsif($rrbs){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	269 deduplicate_barcoded_rrbs($file);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	270 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	271
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	272 ### as the default option we simply write out the first read for a position and discard all others. This is the fastest option
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	273 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	274
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	275 my %unique_seqs;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	276 my %positions;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	277
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	278 if ($file =~ /\.gz$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	279 open (IN,"gunzip -c $file \|") or die "Unable to read from gzipped file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	280 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	281 elsif ($file =~ /\.bam$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	282 open (IN,"$samtools_path view -h $file \|") or die "Unable to read from BAM file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	283 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	284 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	285 open (IN,$file) or die "Unable to read from $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	286 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	287
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	288 my $outfile = $file;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	289 $outfile =~ s/\.gz$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	290 $outfile =~ s/\.sam$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	291 $outfile =~ s/\.bam$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	292 $outfile =~ s/\.txt$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	293
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	294 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	295 $outfile =~ s/$/_deduplicated.txt/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	296 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	297 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	298 if ($bam == 1){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	299 $outfile =~ s/$/.deduplicated.bam/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	300 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	301 elsif ($bam == 2){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	302 $outfile =~ s/$/.deduplicated.sam.gz/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	303 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	304 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	305 $outfile =~ s/$/.deduplicated.sam/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	306 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	307 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	308 if ($bam == 1){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	309 open (OUT,"\| $samtools_path view -bSh 2>/dev/null - > $outfile") or die "Failed to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	310 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	311 elsif($bam == 2){ ### no Samtools found on system. Using GZIP compression instead
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	312 open (OUT,"\| gzip -c - > $outfile") or die "Failed to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	313 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	314
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	315 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	316 open (OUT,'>',$outfile) or die "Unable to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	317 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	318
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	319 ### need to proceed slightly differently for the custom Bismark and Bismark SAM output
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	320 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	321 $_ = <IN>; # Bismark version header
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	322 print OUT; # Printing the Bismark version to the de-duplicated file again
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	323 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	324 my $count = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	325 my $unique_seqs = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	326 my $removed = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	327
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	328 while (<IN>){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	329
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	330 if ($count == 0){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	331 if ($_ =~ /^Bismark version:/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	332 warn "The file appears to be in the custom Bismark and not SAM format. Please see option --vanilla!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	333 sleep (2);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	334 print_helpfile();
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	335 exit;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	336 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	337 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	338
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	339 ### if this was a SAM file we ignore header lines
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	340 unless ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	341 if (/^\@\w{2}\t/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	342 print "skipping header line:\t$_";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	343 print OUT "$_"; # Printing the header lines again into the de-duplicated file
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	344 next;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	345 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	346 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	347
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	348 ++$count;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	349 my $composite; # storing positional data. For single end data we are only using the start coordinate since the end might have been trimmed to different lengths
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	350
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	351 my ($strand,$chr,$start,$end,$cigar);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	352 my $line1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	353
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	354 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	355 ($strand,$chr,$start,$end) = (split (/\t/))[1,2,3,4];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	356 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	357 else{ # SAM format
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	358 ($strand,$chr,$start,$cigar) = (split (/\t/))[1,2,3,5]; # we are assigning the FLAG value to $strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	359
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	360 ### SAM single-end
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	361 if ($single){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	362
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	363 if ($strand == 0 ){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	364 ### read aligned to the forward strand. No action needed
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	365 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	366 elsif ($strand == 16){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	367 ### read is on reverse strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	368
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	369 $start -= 1; # only need to adjust this once
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	370
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	371 # for InDel free matches we can simply use the M number in the CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	372 if ($cigar =~ /^(\d+)M$/){ # linear match
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	373 $start += $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	374 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	375
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	376 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	377 # parsing CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	378 my @len = split (/\D+/,$cigar); # storing the length per operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	379 my @ops = split (/\d+/,$cigar); # storing the operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	380 shift @ops; # remove the empty first element
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	381 die "CIGAR string contained a non-matching number of lengths and operations\n" unless (scalar @len == scalar @ops);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	382
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	383 # warn "CIGAR string; $cigar\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	384 ### determining end position of a read
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	385 foreach my $index(0..$#len){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	386 if ($ops[$index] eq 'M'){ # standard matching bases
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	387 $start += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	388 # warn "Operation is 'M', adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	389 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	390 elsif($ops[$index] eq 'I'){ # insertions do not affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	391 # warn "Operation is 'I', next\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	392 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	393 elsif($ops[$index] eq 'D'){ # deletions do affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	394 # warn "Operation is 'D',adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	395 $start += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	396 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	397 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	398 die "Found CIGAR operations other than M, I or D: '$ops[$index]'. Not allowed at the moment\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	399 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	400 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	401 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	402 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	403 $composite = join (":",$strand,$chr,$start);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	404 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	405 elsif($paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	406
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	407 ### storing the current line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	408 $line1 = $_;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	409
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	410 my $read_conversion;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	411 my $genome_conversion;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	412
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	413 while ( /(XR\|XG):Z:([^\t]+)/g ) {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	414 my $tag = $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	415 my $value = $2;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	416
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	417 if ($tag eq "XR") {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	418 $read_conversion = $value;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	419 $read_conversion =~ s/\r//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	420 chomp $read_conversion;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	421 } elsif ($tag eq "XG") {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	422 $genome_conversion = $value;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	423 $genome_conversion =~ s/\r//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	424 chomp $genome_conversion;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	425 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	426 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	427 die "Failed to determine read and genome conversion from line: $line1\n\n" unless ($read_conversion and $read_conversion);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	428
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	429
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	430 my $index;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	431 if ($read_conversion eq 'CT' and $genome_conversion eq 'CT') { ## original top strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	432 $index = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	433 $strand = '+';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	434 } elsif ($read_conversion eq 'GA' and $genome_conversion eq 'CT') { ## complementary to original top strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	435 $index = 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	436 $strand = '-';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	437 } elsif ($read_conversion eq 'GA' and $genome_conversion eq 'GA') { ## complementary to original bottom strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	438 $index = 2;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	439 $strand = '+';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	440 } elsif ($read_conversion eq 'CT' and $genome_conversion eq 'GA') { ## original bottom strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	441 $index = 3;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	442 $strand = '-';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	443 } else {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	444 die "Unexpected combination of read and genome conversion: '$read_conversion' / '$genome_conversion'\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	445 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	446
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	447 # if the read aligns in forward orientation we can certainly use the start position of read 1, and only need to work out the end position of read 2
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	448 if ($index == 0 or $index == 2){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	449
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	450 ### reading in the next line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	451 $_ = <IN>;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	452 # the only thing we need is the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	453 ($end,my $cigar_2) = (split (/\t/))[3,5];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	454
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	455 $end -= 1; # only need to adjust this once
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	456
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	457 # for InDel free matches we can simply use the M number in the CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	458 if ($cigar_2 =~ /^(\d+)M$/){ # linear match
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	459 $end += $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	460 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	461 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	462 # parsing CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	463 my @len = split (/\D+/,$cigar_2); # storing the length per operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	464 my @ops = split (/\d+/,$cigar_2); # storing the operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	465 shift @ops; # remove the empty first element
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	466 die "CIGAR string contained a non-matching number of lengths and operations ($cigar_2)\n" unless (scalar @len == scalar @ops);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	467
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	468 # warn "CIGAR string; $cigar_2\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	469 ### determining end position of the read
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	470 foreach my $index(0..$#len){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	471 if ($ops[$index] eq 'M'){ # standard matching bases
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	472 $end += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	473 # warn "Operation is 'M', adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	474 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	475 elsif($ops[$index] eq 'I'){ # insertions do not affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	476 # warn "Operation is 'I', next\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	477 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	478 elsif($ops[$index] eq 'D'){ # deletions do affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	479 # warn "Operation is 'D',adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	480 $end += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	481 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	482 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	483 die "Found CIGAR operations other than M, I or D: '$ops[$index]'. Not allowed at the moment\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	484 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	485 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	486 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	487 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	488 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	489 # else read 1 aligns in reverse orientation and we need to work out the end of the fragment first, and use the start of the next line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	490
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	491 $end = $start - 1; # need to adjust this only once
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	492
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	493 # for InDel free matches we can simply use the M number in the CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	494 if ($cigar =~ /^(\d+)M$/){ # linear match
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	495 $end += $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	496 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	497 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	498 # parsing CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	499 my @len = split (/\D+/,$cigar); # storing the length per operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	500 my @ops = split (/\d+/,$cigar); # storing the operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	501 shift @ops; # remove the empty first element
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	502 die "CIGAR string contained a non-matching number of lengths and operations ($cigar)\n" unless (scalar @len == scalar @ops);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	503
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	504 # warn "CIGAR string; $cigar\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	505 ### determining end position of the read
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	506 foreach my $index(0..$#len){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	507 if ($ops[$index] eq 'M'){ # standard matching bases
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	508 $end += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	509 # warn "Operation is 'M', adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	510 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	511 elsif($ops[$index] eq 'I'){ # insertions do not affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	512 # warn "Operation is 'I', next\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	513 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	514 elsif($ops[$index] eq 'D'){ # deletions do affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	515 # warn "Operation is 'D',adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	516 $end += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	517 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	518 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	519 die "Found CIGAR operations other than M, I or D: '$ops[$index]'. Not allowed at the moment\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	520 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	521 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	522 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	523
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	524 ### reading in the next line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	525 $_ = <IN>;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	526 # the only thing we need is the start position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	527 ($start) = (split (/\t/))[3];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	528 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	529 $composite = join (":",$strand,$chr,$start,$end);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	530 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	531
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	532 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	533 die "Input must be single or paired-end\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	534 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	535 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	536
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	537 if (exists $unique_seqs{$composite}){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	538 ++$removed;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	539 unless (exists $positions{$composite}){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	540 $positions{$composite}++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	541 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	542 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	543 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	544 if ($paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	545 unless ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	546 print OUT "$line1"; # printing first paired-end line for SAM output
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	547 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	548 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	549 print OUT "$_"; # printing single-end SAM alignment or second paired-end line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	550 $unique_seqs{$composite}++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	551 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	552 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	553
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	554 my $percentage;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	555 my $percentage_leftover;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	556 my $leftover = $count - $removed;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	557
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	558 unless ($count == 0){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	559 $percentage = sprintf("%.2f",$removed/$count*100);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	560 $percentage_leftover = sprintf("%.2f",$leftover/$count*100);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	561 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	562 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	563 $percentage = 'N/A';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	564 $percentage_leftover = 'N/A';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	565 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	566
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	567 warn "\nTotal number of alignments analysed in $file:\t$count\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	568 warn "Total number duplicated alignments removed:\t$removed ($percentage%)\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	569 warn "Duplicated alignments were found at:\t",scalar keys %positions," different position(s)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	570 warn "Total count of deduplicated leftover sequences: $leftover ($percentage_leftover% of total)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	571
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	572 print REPORT "\nTotal number of alignments analysed in $file:\t$count\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	573 print REPORT "Total number duplicated alignments removed:\t$removed ($percentage%)\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	574 print REPORT "Duplicated alignments were found at:\t",scalar keys %positions," different position(s)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	575 print REPORT "Total count of deduplicated leftover sequences: $leftover ($percentage_leftover% of total)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	576 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	577
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	578 close OUT or warn "Failed to close output filehandle: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	579 close REPORT or warn "Failed to close report filehandle: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	580
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	581 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	582
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	583
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	584 sub deduplicate_barcoded_rrbs{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	585
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	586 my $file = shift;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	587
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	588 my %unique_seqs;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	589 my %positions;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	590
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	591 if ($file =~ /\.gz$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	592 open (IN,"gunzip -c $file \|") or die "Unable to read from gzipped file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	593 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	594 elsif ($file =~ /\.bam$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	595 open (IN,"$samtools_path view -h $file \|") or die "Unable to read from BAM file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	596 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	597 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	598 open (IN,$file) or die "Unable to read from $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	599 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	600
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	601 my $outfile = $file;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	602 $outfile =~ s/\.gz$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	603 $outfile =~ s/\.sam$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	604 $outfile =~ s/\.bam$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	605 $outfile =~ s/\.txt$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	606
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	607 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	608 $outfile =~ s/$/_dedup_RRBS.txt/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	609 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	610 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	611 if ($bam == 1){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	612 $outfile =~ s/$/.dedup_RRBS.bam/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	613 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	614 elsif ($bam == 2){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	615 $outfile =~ s/$/.dedupRRBS.sam.gz/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	616 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	617 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	618 $outfile =~ s/$/.dedup_RRBS.sam/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	619 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	620 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	621 if ($bam == 1){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	622 open (OUT,"\| $samtools_path view -bSh 2>/dev/null - > $outfile") or die "Failed to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	623 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	624 elsif($bam == 2){ ### no Samtools found on system. Using GZIP compression instead
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	625 open (OUT,"\| gzip -c - > $outfile") or die "Failed to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	626 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	627 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	628 open (OUT,'>',$outfile) or die "Unable to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	629 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	630
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	631 ### This mode only supports Bismark SAM output
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	632 my $count = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	633 my $unique_seqs = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	634 my $removed = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	635
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	636 while (<IN>){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	637
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	638 if ($count == 0){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	639 if ($_ =~ /^Bismark version:/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	640 warn "The file appears to be in the custom Bismark and not SAM format. Please see option --vanilla!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	641 sleep (2);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	642 print_helpfile();
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	643 exit;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	644 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	645 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	646
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	647 ### if this was a SAM file we ignore header lines
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	648 if (/^\@\w{2}\t/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	649 warn "skipping SAM header line:\t$_";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	650 print OUT; # Printing the header lines again into the de-duplicated file
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	651 next;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	652 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	653
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	654 ++$count;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	655 my $composite; # storing positional data. For single end data we are only using the start coordinate since the end might have been trimmed to different lengths
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	656 ### in this barcoded mode we also store the read barcode as additional means of assisting the deduplication
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	657 ### in effect the $composite string looks like this (separated by ':'):
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	658
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	659 ### FLAG:chromosome:start:barcode
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	660
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	661 my $end;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	662 my $line1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	663
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	664 # SAM format
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	665 my ($id,$strand,$chr,$start,$cigar) = (split (/\t/))[0,1,2,3,5]; # we are assigning the FLAG value to $strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	666
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	667 $id =~ /:(\w+)$/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	668 my $barcode = $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	669 unless ($barcode){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	670 die "Failed to extract a barcode from the read ID (last element of each read ID needs to be the barcode sequence, e.g. ':CATG'\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	671 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	672
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	673 ### SAM single-end
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	674 if ($single){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	675
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	676 if ($strand == 0 ){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	677 ### read aligned to the forward strand. No action needed
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	678 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	679 elsif ($strand == 16){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	680 ### read is on reverse strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	681
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	682 $start -= 1; # only need to adjust this once
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	683
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	684 # for InDel free matches we can simply use the M number in the CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	685 if ($cigar =~ /^(\d+)M$/){ # linear match
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	686 $start += $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	687 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	688 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	689 # parsing CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	690 my @len = split (/\D+/,$cigar); # storing the length per operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	691 my @ops = split (/\d+/,$cigar); # storing the operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	692 shift @ops; # remove the empty first element
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	693 die "CIGAR string contained a non-matching number of lengths and operations\n" unless (scalar @len == scalar @ops);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	694
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	695 # warn "CIGAR string; $cigar\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	696 ### determining end position of a read
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	697 foreach my $index(0..$#len){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	698 if ($ops[$index] eq 'M'){ # standard matching bases
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	699 $start += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	700 # warn "Operation is 'M', adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	701 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	702 elsif($ops[$index] eq 'I'){ # insertions do not affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	703 # warn "Operation is 'I', next\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	704 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	705 elsif($ops[$index] eq 'D'){ # deletions do affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	706 # warn "Operation is 'D',adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	707 $start += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	708 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	709 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	710 die "Found CIGAR operations other than M, I or D: '$ops[$index]'. Not allowed at the moment\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	711 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	712 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	713 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	714 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	715
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	716 ### Here we take the barcode sequence into consideration
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	717 $composite = join (":",$strand,$chr,$start,$barcode);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	718 # warn "$composite\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	719 # sleep(1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	720 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	721 elsif($paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	722
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	723 ### storing the current line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	724 $line1 = $_;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	725
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	726 my $read_conversion;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	727 my $genome_conversion;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	728
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	729 while ( /(XR\|XG):Z:([^\t]+)/g ) {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	730 my $tag = $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	731 my $value = $2;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	732
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	733 if ($tag eq "XR") {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	734 $read_conversion = $value;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	735 $read_conversion =~ s/\r//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	736 chomp $read_conversion;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	737 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	738 elsif ($tag eq "XG") {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	739 $genome_conversion = $value;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	740 $genome_conversion =~ s/\r//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	741 chomp $genome_conversion;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	742 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	743 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	744 die "Failed to determine read and genome conversion from line: $line1\n\n" unless ($read_conversion and $read_conversion);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	745
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	746
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	747 my $index;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	748 if ($read_conversion eq 'CT' and $genome_conversion eq 'CT') { ## original top strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	749 $index = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	750 $strand = '+';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	751 } elsif ($read_conversion eq 'GA' and $genome_conversion eq 'CT') { ## complementary to original top strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	752 $index = 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	753 $strand = '-';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	754 } elsif ($read_conversion eq 'GA' and $genome_conversion eq 'GA') { ## complementary to original bottom strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	755 $index = 2;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	756 $strand = '+';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	757 } elsif ($read_conversion eq 'CT' and $genome_conversion eq 'GA') { ## original bottom strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	758 $index = 3;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	759 $strand = '-';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	760 } else {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	761 die "Unexpected combination of read and genome conversion: '$read_conversion' / '$genome_conversion'\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	762 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	763
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	764 # if the read aligns in forward orientation we can certainly use the start position of read 1, and only need to work out the end position of read 2
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	765 if ($index == 0 or $index == 2){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	766
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	767 ### reading in the next line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	768 $_ = <IN>;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	769 # the only thing we need is the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	770 ($end,my $cigar_2) = (split (/\t/))[3,5];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	771
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	772 $end -= 1; # only need to adjust this once
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	773
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	774 # for InDel free matches we can simply use the M number in the CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	775 if ($cigar_2 =~ /^(\d+)M$/){ # linear match
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	776 $end += $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	777 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	778 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	779 # parsing CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	780 my @len = split (/\D+/,$cigar_2); # storing the length per operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	781 my @ops = split (/\d+/,$cigar_2); # storing the operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	782 shift @ops; # remove the empty first element
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	783 die "CIGAR string contained a non-matching number of lengths and operations ($cigar_2)\n" unless (scalar @len == scalar @ops);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	784
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	785 # warn "CIGAR string; $cigar_2\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	786 ### determining end position of the read
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	787 foreach my $index(0..$#len){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	788 if ($ops[$index] eq 'M'){ # standard matching bases
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	789 $end += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	790 # warn "Operation is 'M', adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	791 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	792 elsif($ops[$index] eq 'I'){ # insertions do not affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	793 # warn "Operation is 'I', next\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	794 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	795 elsif($ops[$index] eq 'D'){ # deletions do affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	796 # warn "Operation is 'D',adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	797 $end += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	798 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	799 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	800 die "Found CIGAR operations other than M, I or D: '$ops[$index]'. Not allowed at the moment\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	801 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	802 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	803 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	804 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	805 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	806 # else read 1 aligns in reverse orientation and we need to work out the end of the fragment first, and use the start of the next line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	807
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	808 $end = $start - 1; # need to adjust this only once
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	809
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	810 # for InDel free matches we can simply use the M number in the CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	811 if ($cigar =~ /^(\d+)M$/){ # linear match
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	812 $end += $1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	813 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	814 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	815 # parsing CIGAR string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	816 my @len = split (/\D+/,$cigar); # storing the length per operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	817 my @ops = split (/\d+/,$cigar); # storing the operation
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	818 shift @ops; # remove the empty first element
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	819 die "CIGAR string contained a non-matching number of lengths and operations ($cigar)\n" unless (scalar @len == scalar @ops);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	820
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	821 # warn "CIGAR string; $cigar\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	822 ### determining end position of the read
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	823 foreach my $index(0..$#len){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	824 if ($ops[$index] eq 'M'){ # standard matching bases
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	825 $end += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	826 # warn "Operation is 'M', adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	827 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	828 elsif($ops[$index] eq 'I'){ # insertions do not affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	829 # warn "Operation is 'I', next\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	830 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	831 elsif($ops[$index] eq 'D'){ # deletions do affect the end position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	832 # warn "Operation is 'D',adding $len[$index] bp\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	833 $end += $len[$index];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	834 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	835 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	836 die "Found CIGAR operations other than M, I or D: '$ops[$index]'. Not allowed at the moment\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	837 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	838 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	839 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	840
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	841 ### reading in the next line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	842 $_ = <IN>;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	843 # the only thing we need is the start position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	844 ($start) = (split (/\t/))[3];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	845 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	846
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	847 ### Here we take the barcode sequence into consideration
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	848 $composite = join (":",$strand,$chr,$start,$end,$barcode);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	849 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	850 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	851 die "Input must be single or paired-end\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	852 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	853
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	854 if (exists $unique_seqs{$composite}){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	855 ++$removed;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	856 unless (exists $positions{$composite}){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	857 $positions{$composite}++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	858 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	859 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	860 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	861 if ($paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	862 print OUT $line1; # printing first paired-end line for SAM output
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	863 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	864 print OUT; # printing single-end SAM alignment or second paired-end line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	865 $unique_seqs{$composite}++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	866 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	867 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	868
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	869 my $percentage;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	870 my $percentage_leftover;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	871 my $leftover = $count - $removed;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	872
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	873 unless ($count == 0){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	874 $percentage = sprintf("%.2f",$removed/$count*100);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	875 $percentage_leftover = sprintf("%.2f",$leftover/$count*100);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	876 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	877 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	878 $percentage = 'N/A';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	879 $percentage_leftover = 'N/A';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	880 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	881
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	882
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	883 warn "\nTotal number of alignments analysed in $file:\t$count\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	884 warn "Total number duplicated alignments removed:\t$removed ($percentage%)\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	885 warn "Duplicated alignments were found at:\t",scalar keys %positions," different position(s)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	886 warn "Total count of deduplicated leftover sequences: $leftover ($percentage_leftover% of total)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	887
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	888 print REPORT "\nTotal number of alignments analysed in $file:\t$count\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	889 print REPORT "Total number duplicated alignments removed:\t$removed ($percentage%)\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	890 print REPORT "Duplicated alignments were found at:\t",scalar keys %positions," different position(s)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	891 print REPORT "Total count of deduplicated leftover sequences: $leftover ($percentage_leftover% of total)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	892
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	893 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	894
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	895 sub bam_isEmpty{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	896
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	897 my $file = shift;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	898
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	899 if ($file =~ /\.bam$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	900 open (EMPTY,"$samtools_path view $file \|") or die "Unable to read from BAM file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	901 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	902 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	903 open (EMPTY,$file) or die "Unable to read from $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	904 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	905 my $count = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	906 while (<EMPTY>){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	907 if ($_){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	908 $count++; # file contains data, fine.
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	909 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	910 last; # one line is enough
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	911 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	912
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	913 if ($count == 0){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	914 die "\n### File appears to be empty, terminating deduplication process. Please make sure the input file has not been truncated. ###\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	915 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	916 close EMPTY or warn "$!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	917 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	918
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	919
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	920 sub print_helpfile{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	921 print "\n",'='x111,"\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	922 print "\nThis script is supposed to remove alignments to the same position in the genome from the Bismark mapping output\n(both single and paired-end SAM files), which can arise by e.g. excessive PCR amplification. If sequences align\nto the same genomic position but on different strands they will be scored individually.\n\nNote that deduplication is not recommended for RRBS-type experiments!\n\nIn the default mode, the first alignment to a given position will be used irrespective of its methylation call\n(this is the fastest option, and as the alignments are not ordered in any way this is also near enough random).\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	923 print "For single-end alignments only use the start coordinate of a read will be used for deduplication.\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	924 print "For paired-end alignments the start-coordinate of the first read and the end coordinate of the second\nread will be used for deduplication. ";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	925 print "This script expects the Bismark output to be in SAM format\n(Bismark v0.6.x or higher). To deduplicate the old custom Bismark output please specify '--vanilla'.\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	926 print "* Please note that for paired-end BAM files the deduplication script expects Read1 and Read2 to\nfollow each other in consecutive lines! If the file has been sorted by position make sure that you resort it\nby read name first (e.g. using samtools sort -n) *\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	927
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	928 print '='x111,"\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	929 print ">>> USAGE: ./deduplicate_bismark_alignment_output.pl [options] filename(s) <<<\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	930
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	931 print "-s/--single\t\tdeduplicate single-end Bismark files (default format: SAM)\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	932 print "-p/--paired\t\tdeduplicate paired-end Bismark files (default format: SAM)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	933 print "--vanilla\t\tThe input file is in the old custom Bismark format and not in SAM format\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	934 print "--barcode\t\tIn addition to chromosome, start position and orientation this will also take a potential barcode into\n consideration while deduplicating. The barcode needs to be the last element of the read ID and separated\n by a ':', e.g.: MISEQ:14:000000000-A55D0:1:1101:18024:2858_1:N:0:CTCCT\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	935 print "--bam\t\t\tThe output will be written out in BAM format instead of the default SAM format. This script will\n\t\t\tattempt to use the path to Samtools that was specified with '--samtools_path', or, if it hasn't\n\t\t\tbeen specified, attempt to find Samtools in the PATH. If no installation of Samtools can be found,\n\t\t\tthe SAM output will be compressed with GZIP instead (yielding a .sam.gz output file)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	936 print "--samtools_path\t\tThe path to your Samtools installation, e.g. /home/user/samtools/. Does not need to be specified\n\t\t\texplicitly if Samtools is in the PATH already\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	937 print "--version\t\tPrint version information and exit\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	938
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	939 print '='x111,"\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	940
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	941 print "This script was last modified on November 04, 2015\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	942 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	943
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	944
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	945
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	946
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	947 sub test_positional_sorting{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	948
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	949 my $filename = shift;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	950
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	951 print "\nNow testing Bismark result file $filename for positional sorting (which would be bad...)\t";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	952 sleep(1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	953
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	954 if ($filename =~ /\.gz$/) {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	955 open (TEST,"gunzip -c $filename \|") or die "Can't open gzipped file $filename: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	956 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	957 elsif ($filename =~ /bam$/ \|\| isBam($filename) ){ ### this would allow to read BAM files that do not end in *.bam
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	958 if ($samtools_path){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	959 open (TEST,"$samtools_path view -h $filename \|") or die "Can't open BAM file $filename: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	960 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	961 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	962 die "Sorry couldn't find an installation of Samtools. Either specifiy an alternative path using the option '--samtools_path /your/path/', or use a SAM file instead\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	963 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	964 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	965 else {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	966 open (TEST,$filename) or die "Can't open file $filename: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	967 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	968
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	969 my $count = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	970
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	971 while (<TEST>) {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	972 if (/^\@/) { # testing header lines if they contain the @SO flag (for being sorted)
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	973 if (/^\@SO/) {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	974 die "SAM/BAM header line '$_' indicates that the Bismark aligment file has been sorted by chromosomal positions which is is incompatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	975 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	976 next;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	977 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	978 $count++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	979
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	980 last if ($count > 100000); # else we test the first 100000 sequences if they start with the same read ID
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	981
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	982 my ($id_1) = (split (/\t/));
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	983
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	984 ### reading the next line which should be read 2
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	985 $_ = <TEST>;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	986 my ($id_2) = (split (/\t/));
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	987 last unless ($id_2);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	988 ++$count;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	989
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	990 if ($id_1 eq $id_2){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	991 ### ids are the same
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	992 next;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	993 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	994 else{ ### in previous versions of Bismark we appended /1 and /2 to the read IDs for easier eyeballing which read is which. These tags need to be removed first
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	995 my $id_1_trunc = $id_1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	996 $id_1_trunc =~ s/\/1$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	997 my $id_2_trunc = $id_2;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	998 $id_2_trunc =~ s/\/2$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	999
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1000 unless ($id_1_trunc eq $id_2_trunc){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1001 die "\nThe IDs of Read 1 ($id_1) and Read 2 ($id_2) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1002 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1003 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1004 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1005 # close TEST or die $!; somehow fails on our cluster...
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1006 ### If it hasen't died so far then it seems the file is in the correct Bismark format (read 1 and read 2 of a pair directly following each other)
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1007 warn "...passed!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1008 sleep(1);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1009
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1010 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1011
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1012 sub isBam{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1013
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1014 my $filename = shift;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1015
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1016 # reading the first line of the input file to see if it is a BAM file in disguise (i.e. a BAM file that does not end in *.bam which may be produced by Galaxy)
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1017 open (DISGUISE,"gunzip -c $filename \|") or die "Failed to open filehandle DISGUISE for $filename\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1018
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1019 ### when BAM files read through a gunzip -c stream they start with BAM...
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1020 my $bam_in_disguise = <DISGUISE>;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1021 # warn "BAM in disguise: $bam_in_disguise\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1022
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1023 if ($bam_in_disguise){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1024 if ($bam_in_disguise =~ /^BAM/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1025 close (DISGUISE) or warn "Had trouble closing filehandle BAM in disguise: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1026 return 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1027 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1028 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1029 close (DISGUISE) or warn "Had trouble closing filehandle BAM in disguise: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1030 return 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1031 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1032 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1033 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1034 close (DISGUISE) or warn "Had trouble closing filehandle BAM in disguise: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1035 return 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1036 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1037 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1038
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1039
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1040
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1041
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1042
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1043 #####################################
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1044
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1045 ### The following subroutine "deduplicate_representative" only works correctly for reads that do not contain any indels (as in only Bowtie1-based alignments).
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1046 ### Please refrain from using it unless you want to test something out.
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1047
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1048 #####################################
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1049
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1050 sub deduplicate_representative {
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1051 my $file = shift;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1052
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1053 my %positions;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1054 my %unique_seqs;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1055
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1056 my $count = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1057 my $unique_seqs = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1058 my $removed = 0;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1059
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1060 ### going through the file first and storing all positions as well as their methylation call strings in a hash
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1061 if ($file =~ /\.gz$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1062 open (IN,"gunzip -c $file \|") or die "Unable to read from gzipped file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1063 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1064 elsif ($file =~ /\.bam$/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1065 open (IN,"$samtools_path view -h $file \|") or die "Unable to read from BAM file $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1066 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1067 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1068 open (IN,$file) or die "Unable to read from $file: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1069 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1070
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1071 if ($single){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1072
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1073 my $outfile = $file;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1074 $outfile =~ s/\.gz$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1075 $outfile =~ s/\.sam$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1076 $outfile =~ s/\.bam$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1077 $outfile =~ s/\.txt$//;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1078
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1079 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1080 $outfile =~ s/$/.deduplicated_to_representative_sequences.txt/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1081 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1082 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1083 if ($bam == 1){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1084 $outfile =~ s/$/.deduplicated_to_representative_sequences.bam/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1085 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1086 elsif ($bam == 2){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1087 $outfile =~ s/$/.deduplicated_to_representative_sequences.sam.gz/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1088 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1089 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1090 $outfile =~ s/$/.deduplicated_to_representative_sequences.sam/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1091 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1092 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1093
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1094 if ($bam == 1){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1095 open (OUT,"\| $samtools_path view -bSh 2>/dev/null - > $outfile") or die "Failed to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1096 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1097 elsif($bam == 2){ ### no Samtools found on system. Using GZIP compression instead
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1098 open (OUT,"\| gzip -c - > $outfile") or die "Failed to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1099 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1100 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1101 open (OUT,'>',$outfile) or die "Unable to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1102 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1103
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1104 warn "Reading and storing all alignment positions\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1105
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1106 ### need to proceed slightly differently for the custom Bismark and Bismark SAM output
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1107 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1108 $_ = <IN>; # Bismark version header
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1109 print OUT; # Printing the Bismark version to the de-duplicated file again
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1110 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1111
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1112 while (<IN>){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1113
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1114 if ($count == 0){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1115 if ($_ =~ /^Bismark version:/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1116 warn "The file appears to be in the custom Bismark and not SAM format. Please see option --vanilla!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1117 sleep (2);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1118 print_helpfile();
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1119 exit;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1120 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1121 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1122
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1123 ### if this was a SAM file we ignore header lines
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1124 unless ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1125 if (/^\@\w{2}\t/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1126 warn "skipping SAM header line:\t$_";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1127 print OUT; # Printing the header lines again into the de-duplicated file
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1128 next;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1129 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1130 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1131
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1132 my ($strand,$chr,$start,$end,$meth_call);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1133
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1134 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1135 ($strand,$chr,$start,$end,$meth_call) = (split (/\t/))[1,2,3,4,7];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1136 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1137 else{ # SAM format
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1138
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1139 ($strand,$chr,$start,my $seq,$meth_call) = (split (/\t/))[1,2,3,9,13]; # we are assigning the FLAG value to $strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1140 ### SAM single-end
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1141 $end = $start + length($seq) - 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1142 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1143
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1144 my $composite = join (":",$strand,$chr,$start,$end);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1145
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1146 $count++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1147 $positions{$composite}->{$meth_call}->{count}++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1148 $positions{$composite}->{$meth_call}->{alignment} = $_;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1149 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1150 warn "Stored ",scalar keys %positions," different positions for $count sequences in total (+ and - alignments to the same position are scored individually)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1151 close IN or warn $!;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1152 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1153
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1154 elsif ($paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1155
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1156 ### we are going to concatenate both methylation call strings from the paired end file to form a joint methylation call string
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1157
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1158 my $outfile = $file;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1159 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1160 $outfile =~ s/$/_deduplicated_to_representative_sequences_pe.txt/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1161 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1162 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1163 $outfile =~ s/$/_deduplicated_to_representative_sequences_pe.sam/;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1164 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1165
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1166 open (OUT,'>',$outfile) or die "Unable to write to $outfile: $!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1167 warn "Reading and storing all alignment positions\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1168
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1169 ### need to proceed slightly differently for the custom Bismark and Bismark SAM output
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1170 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1171 $_ = <IN>; # Bismark version header
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1172 print OUT; # Printing the Bismark version to the de-duplicated file again
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1173 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1174
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1175 while (<IN>){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1176
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1177 if ($count == 0){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1178 if ($_ =~ /^Bismark version:/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1179 warn "The file appears to be in the custom Bismark and not SAM format. Please see option --vanilla!\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1180 sleep (2);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1181 print_helpfile();
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1182 exit;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1183 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1184 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1185
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1186 ### if this was a SAM file we ignore header lines
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1187 unless ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1188 if (/^\@\w{2}\t/){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1189 warn "skipping SAM header line:\t$_";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1190 print OUT; # Printing the header lines again into the de-duplicated file
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1191 next;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1192 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1193 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1194
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1195 my ($strand,$chr,$start,$end,$meth_call_1,$meth_call_2);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1196 my $line1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1197
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1198 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1199 ($strand,$chr,$start,$end,$meth_call_1,$meth_call_2) = (split (/\t/))[1,2,3,4,7,10];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1200 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1201 else{ # SAM paired-end format
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1202
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1203 ($strand,$chr,$start,$meth_call_1) = (split (/\t/))[1,2,3,13]; # we are assigning the FLAG value to $strand
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1204
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1205 ### storing the first line (= read 1 alignment)
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1206 $line1 = $_;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1207
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1208 ### reading in the next line
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1209 $_ = <IN>;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1210 # we only need the end position and the methylation call
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1211 (my $pos,my $seq_2,$meth_call_2) = (split (/\t/))[3,9,13];
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1212 $end = $pos + length($seq_2) - 1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1213 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1214
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1215 my $composite = join (":",$strand,$chr,$start,$end);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1216 $count++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1217 my $meth_call = $meth_call_1.$meth_call_2;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1218
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1219 $positions{$composite}->{$meth_call}->{count}++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1220 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1221 $positions{$composite}->{$meth_call}->{alignment} = $_;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1222 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1223 else{ # SAM PAIRED-END
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1224 $positions{$composite}->{$meth_call}->{alignment_1} = $line1;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1225 $positions{$composite}->{$meth_call}->{alignment_2} = $_;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1226 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1227 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1228 warn "Stored ",scalar keys %positions," different positions for $count sequences in total (+ and - alignments to the same position are scored individually)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1229 close IN or warn $!;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1230 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1231
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1232 ### PRINTING RESULTS
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1233
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1234 ### Now going through all stored positions and printing out the methylation call which is most representative, i.e. the one which occurred most often
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1235 warn "Now printing out alignments with the most representative methylation call(s)\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1236
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1237 foreach my $pos (keys %positions){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1238 foreach my $meth_call (sort { $positions{$pos}->{$b}->{count} <=> $positions{$pos}->{$a}->{count} }keys %{$positions{$pos}}){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1239 if ($paired){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1240 if ($vanilla){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1241 print OUT $positions{$pos}->{$meth_call}->{alignment};
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1242 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1243 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1244 print OUT $positions{$pos}->{$meth_call}->{alignment_1}; # SAM read 1
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1245 print OUT $positions{$pos}->{$meth_call}->{alignment_2}; # SAM read 2
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1246 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1247 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1248 else{ # single-end
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1249 print OUT $positions{$pos}->{$meth_call}->{alignment};
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1250 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1251 $unique_seqs++;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1252 last; ### exiting once we printed a sequence with the most frequent methylation call for a position
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1253 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1254 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1255
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1256 my $percentage;
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1257 unless ($count == 0){
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1258 $percentage = sprintf ("%.2f",$unique_seqs*100/$count);
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1259 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1260 else{
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1261 $percentage = 'N/A';
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1262 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1263
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1264 warn "\nTotal number of alignments analysed in $file:\t$count\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1265 warn "Total number of representative alignments printed from $file in total:\t$unique_seqs ($percentage%)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1266 print REPORT "\nTotal number of alignments analysed in $file:\t$count\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1267 print REPORT "Total number of representative alignments printed from $file in total:\t$unique_seqs ($percentage%)\n\n";
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1268
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1269 }
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1270
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1271
b2b75548b4eb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: diff changeset	1272

Mercurial > repos > bgruening > bismark

annotate bismark_deduplicate/deduplicate_bismark @ 24:b2b75548b4eb draft