# HG changeset patch
# User pitagora
# Date 1410504192 14400
# Node ID b500f5f3c988d7cc0604a52025fb87a2f2970b07
# Parent  4ebcbb69142627778cf8a27a11d25a84c75d0dca
Deleted selected files

diff -r 4ebcbb691426 -r b500f5f3c988 export2sam/export2sam.sh
--- a/export2sam/export2sam.sh	Fri Sep 12 02:42:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-#!/bin/sh
-# SET TOOL DIRECTORY
-
-CMDNAME=`basename $0`
-
-while getopts a:b:o:gr OPT
-do
-  case $OPT in
-    "a" ) FLG_A="TRUE" ; VALUE_A="$OPTARG" ;;
-    "b" ) FLG_B="TRUE" ; VALUE_B="$OPTARG" ;;
-    "o" ) FLG_O="TRUE" ; VALUE_O="$OPTARG" ;;
-    "g" ) FLG_G="TRUE" ;;
-    "r" ) FLG_R="TRUE" ;;
-      * ) echo "Usage: $CMDNAME [-a VALUE] [-b] [-o VALUE] [-gr]" 1>&2
-          exit 1 ;;
-  esac
-done
-
-# SINGLE END OR PAIR END
-if [ ! $FLG_B ] ; then
-  ARGS="--read1=$VALUE_A"
-else
-  ARGS="--read1=$VALUE_A --read2=$VALUE_B"
-fi
-
-# GZIPPED OR NOT
-if [ $FLG_G ] ; then
-  CMD1="./illumina_export2sam_gz.pl $ARGS"
-else
-  CMD1="./illumina_export2sam.pl $ARGS"
-fi
-
-# MODIFY ACCORDING TO THE REFERENCE
-if [ $FLG_R ] ; then
-  CMD2='$tmp=$_;$tmp=~s/chr_fragments\.fa\///g;$tmp=~s/(chr\w+)\.fa/$1/g;print $tmp;'
-  CMD="$CMD1 | perl -ne '$CMD2'"
-else
-  CMD=$CMD1
-fi
-
-echo $CMD
-eval $CMD > $VALUE_O
diff -r 4ebcbb691426 -r b500f5f3c988 export2sam/export2sam.xml
--- a/export2sam/export2sam.xml	Fri Sep 12 02:42:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<tool id="export2sam" name="Export to SAM" version="0.1">
-  <description></description>
-  <parallelism method="basic"></parallelism>
-  <command interpreter="sh">
-    export2sam.sh
-      -a $read1
-      #if $pairCondition.pairSelect == "yes"
-        -b $read2
-      #end if
-      -o $output
-      $gunzip
-      $remove
-  </command>
-  <inputs>
-    <param name="read1" type="data" format="eland_export" label="ELAND export file" help="" />
-    <param name="gunzip" type="boolean" truevalue="-g" falsevalue="" checked="True" label="Input file is gzipped" help="" />
-    <param name="remove" type="boolean" truevalue="-r" falsevalue="" checked="True" label="Remove (chr).fa and chr_fragments.fa/" help="" />
-    <conditional name="pairCondition">
-      <param name="pairSelect" type="select" label="Pair end?">
-        <option value="yes">Yes</option>
-        <option value="no" selected="True">No</option>
-      </param>
-      <when value="yes">
-        <param name="read2" type="data" format="eland_export" label="ELAND export file" help="" />
-      </when>
-      <when value="no"></when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data format="sam" name="output" label="${tool.name} on ${on_string}"/>
-  </outputs>
-  <help>If thou thyself canst do it, attend no other's help or hand.</help>
-</tool>
diff -r 4ebcbb691426 -r b500f5f3c988 export2sam/illumina_export2sam.pl
--- a/export2sam/illumina_export2sam.pl	Fri Sep 12 02:42:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,562 +0,0 @@
-#!/usr/bin/env perl
-#
-#
-# illumina_export2sam.pl converts GERALD export files to SAM format.
-#
-#
-#
-########## License:
-#
-# The MIT License
-#
-# Original SAMtools work copyright (c) 2008-2009 Genome Research Ltd.
-# Modified SAMtools work copyright (c) 2010 Illumina, Inc.
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-# 
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-#
-#
-########## Additional notice for CASAVA installation:
-#
-# This file [illumina_export2sam.pl] in the CASAVA installation has
-# been copied from the file [export2sam.pl] in the SAMtools package
-# and modified by Illumina as permitted under the MIT license that
-# governs SAMtools. Illumina recommends the use of the modified
-# version to convert data from the Illumina export format to the SAM
-# file format. The terms of the MIT license specify your right to
-# further modify and distribute the SAMtools code. For the avoidance
-# of doubt, your rights with respect to copying, modifying, using and
-# distributing CASAVA are more restricted than the rights in the MIT
-# license, and are set forth in the Illumina Genome Analyzer Software
-# License Agreement and the Illumina Source Code License Agreement.
-#
-########## ChangeLog:
-#
-# Version: 2.3.1 (18MAR2011)
-#
-#   - Restore file '-' as stdin input.
-#
-# Version: 2.3.0 (24JAN2011)
-#
-#   - Add support for export reserved chromosome name "CONTROL",
-#       which is translated to optional field "XC:Z:CONTROL".
-#   - Check for ".gz" file extension on export files and open
-#       these as gzip pipes when the extension is found.
-#
-# Version: 2.2.0 (16NOV2010)
-#
-#   - Remove any leading zeros in export fields: RUNNO,LANE,TILE,X,Y
-#   - For export records with reserved chromosome name identifiers
-#       "QC" and "RM", add the optional field "XC:Z:QC" or "XC:Z:RM"
-#       to the SAM record, so that these cases can be distinguished
-#       from other unmatched reads.
-#
-# Version: 2.1.0 (21SEP2010)
-#
-#   - Additional export record error checking.
-#   - Convert export records with chromosome value of "RM" to unmapped
-#       SAM records.
-#
-# Version: 2.0.0 (15FEB2010)
-#
-#   Script updated by Illumina in conjunction with CASAVA 1.7.0
-#   release.
-#
-#   Major changes are as follows:
-#   - The CIGAR string has been updated to include all gaps from
-#       ELANDv2 alignments.
-#   - The ELAND single read alignment score is always stored in the
-#       optional "SM" field and the ELAND paired read alignment score
-#       is stored in the optional "AS" field when it exists.
-#   - The MAPQ value is set to the higher of the two alignment scores,
-#       but no greater than 254, i.e. min(254,max(SM,AS))
-#   - The SAM "proper pair" bit (0x0002) is now set for read pairs
-#       meeting ELAND's expected orientation and insert size criteria.
-#   - The default quality score translation is set for export files
-#       which contain Phread+64 quality values. An option,
-#       "--qlogodds", has been added to translate quality values from
-#       the Solexa+64 format used in export files prior to Pipeline
-#       1.3
-#   - The export match descriptor is now reverse-complemented when
-#       necessary such that it always corresponds to the forward
-#       strand of the reference, to be consistent with other
-#       information in the SAM record. It is now written to the
-#       optional 'XD' field (rather than 'MD') to acknowledge its
-#       minor differences from the samtools match descriptor (see
-#       additional detail below).
-#   - An option, "--nofilter", has been added to include reads which
-#       have failed primary analysis quality filtration. Such reads
-#       will have the corresponding SAM flag bit (0x0200) set.
-#   - Labels in the export 'contig' field are preserved by setting
-#       RNAME to "$export_chromosome/$export_contig" when the contig
-#       label exists.
-#
-#
-# Contact: lh3
-# Version: 0.1.2 (03JAN2009)
-#
-#
-#
-########## Known Conversion Limitations:
-#
-# - Export records for reads that map to a position < 1 (allowed
-#     in export format), are converted to unmapped reads in the SAM
-#     record.
-# - Export records contain the reserved chromosome names: "NM",
-#     "QC","RM" and "CONTROL". "NM" indicates that the aligner could
-#     not map the read to the reference sequence set. "QC" means that
-#     the aligner did not attempt to map the read due to some
-#     technical limitation. "RM" means that the read mapped to a set
-#     of 'contaminant' sequences specified in GERALD's RNA-seq
-#     workflow. "CONTROL" means that the read is a control. All of
-#     these alignment types are collapsed to the single unmapped
-#     alignment state in the SAM record, but the optional SAM "XC"
-#     field is used to record the original reserved chromosome name of
-#     the read for all but the "NM" case.
-# - The export match descriptor is slightly different than the
-#     samtools match descriptor. For this reason it is stored in the
-#     optional SAM field 'XD' (and not 'MD'). Note that the export
-#     match descriptor differs from the samtools version in two
-#     respects: (1) indels are explicitly closed with the '$'
-#     character and (2) insertions must be enumerated in the match
-#     descriptor. For example a 35-base read with a two-base insertion
-#     is described as: 20^2$14
-#
-#
-#
-
-my $version = "2.3.1";
-
-use strict;
-use warnings;
-
-use Getopt::Long;
-use File::Spec;
-use List::Util qw(min max);
-
-
-use constant {
-  EXPORT_MACHINE => 0,
-  EXPORT_RUNNO => 1,
-  EXPORT_LANE => 2,
-  EXPORT_TILE => 3,
-  EXPORT_X => 4,
-  EXPORT_Y => 5,
-  EXPORT_INDEX => 6,
-  EXPORT_READNO => 7,
-  EXPORT_READ => 8,
-  EXPORT_QUAL => 9,
-  EXPORT_CHROM => 10,
-  EXPORT_CONTIG => 11,
-  EXPORT_POS => 12,
-  EXPORT_STRAND => 13, 
-  EXPORT_MD => 14,
-  EXPORT_SEMAP => 15,
-  EXPORT_PEMAP => 16,
-  EXPORT_PASSFILT => 21,
-  EXPORT_SIZE => 22,
-};
-
-
-use constant {
-  SAM_QNAME => 0,
-  SAM_FLAG => 1,
-  SAM_RNAME => 2,
-  SAM_POS => 3,
-  SAM_MAPQ => 4,
-  SAM_CIGAR => 5,
-  SAM_MRNM => 6,
-  SAM_MPOS => 7,
-  SAM_ISIZE => 8,
-  SAM_SEQ => 9,
-  SAM_QUAL => 10,
-};
-
-
-# function prototypes for Richard's code
-sub match_desc_to_cigar($);
-sub match_desc_frag_length($);
-sub reverse_compl_match_descriptor($);
-sub write_header($;$;$);
-
-
-&export2sam;
-exit;
-
-
-
-
-sub export2sam {
-
-  my $cmdline = $0 . " " . join(" ",@ARGV);
-  my $arg_count = scalar @ARGV;
-  my $progname = "illumina_export2sam.pl";
-
-  my $is_logodds_qvals = 0; # if true, assume files contain logodds (i.e. "solexa") quality values
-  my $is_nofilter = 0;
-  my $read1file;
-  my $read2file;
-  my $print_version = 0;
-  my $help = 0;
-
-  my $result = GetOptions( "qlogodds" => \$is_logodds_qvals, 
-                           "nofilter" => \$is_nofilter,
-                           "read1=s"  => \$read1file,
-                           "read2=s"  => \$read2file,
-                           "version"  => \$print_version,
-                           "help"     => \$help );
-
-  my $usage = <<END;
-
-$progname converts GERALD export files to SAM format.
-
-Usage: $progname --read1=FILENAME [ options ] | --version | --help
-
-  --read1=FILENAME  read1 export file or '-' for stdin (mandatory)
-                      (file may be gzipped with ".gz" extension)
-  --read2=FILENAME  read2 export file or '-' for stdin
-                      (file may be gzipped with ".gz" extension)
-  --nofilter        include reads that failed the basecaller
-                      purity filter
-  --qlogodds        assume export file(s) use logodds quality values
-                      as reported by OLB (Pipeline) prior to v1.3
-                      (default: phred quality values)
-
-END
-
-  my $version_msg = <<END;
-
-$progname version: $version
-
-END
-
-  if((not $result) or $help or ($arg_count==0)) {
-    die($usage);
-  }
-
-  if(@ARGV) {
-    print STDERR "\nERROR: Unrecognized arguments: " . join(" ",@ARGV) . "\n\n";
-    die($usage);
-  }
-
-  if($print_version) {
-    die($version_msg);
-  }
-
-  if(not defined($read1file)) {
-    print STDERR "\nERROR: read1 export file must be specified\n\n";
-    die($usage);
-  }
-
-  unless((-f $read1file) or ($read1file eq '-')) {
-    die("\nERROR: Can't find read1 export file: '$read1file'\n\n");
-  }
-
-  if (defined $read2file) {
-    unless((-f $read2file) or ($read2file eq '-')) {
-      die("\nERROR: Can't find read2 export file: '$read2file'\n\n");
-    }
-    if($read1file eq $read2file) {
-      die("\nERROR: read1 and read2 export filenames are the same: '$read1file'\n\n");
-    }
-  }
-
-  my ($fh1, $fh2, $is_paired);
-
-  my $read1cmd="$read1file";
-  $read1cmd = "gzip -dc $read1file |" if($read1file =~ /\.gz$/);
-  open($fh1, $read1cmd)
-      or die("\nERROR: Can't open read1 process: '$read1cmd'\n\n");
-  $is_paired = defined $read2file;
-  if ($is_paired) {
-    my $read2cmd="$read2file";
-    $read2cmd = "gzip -dc $read2file |" if($read2file =~ /\.gz$/);
-    open($fh2, $read2cmd)
-        or die("\nERROR: Can't open read2 process: '$read2cmd'\n\n");
-  }
-  # quality value conversion table
-  my @conv_table;
-  if($is_logodds_qvals){ # convert from solexa+64 quality values (pipeline pre-v1.3):
-    for (-64..64) {
-      $conv_table[$_+64] = int(33 + 10*log(1+10**($_/10.0))/log(10)+.499);
-    }
-  } else {               # convert from phred+64 quality values (pipeline v1.3+):
-    for (-64..-1) {
-      $conv_table[$_+64] = undef;
-    }
-    for (0..64) {
-      $conv_table[$_+64] = int(33 + $_);
-    }
-  }
-  # write the header
-  print write_header( $progname, $version, $cmdline );
-  # core loop
-  my $export_line_count = 0;
-  while (<$fh1>) {
-    $export_line_count++;
-    my (@s1, @s2);
-    &export2sam_aux($_, $export_line_count, \@s1, \@conv_table, $is_paired, 1, $is_nofilter);
-    if ($is_paired) {
-      my $read2line = <$fh2>;
-      if(not $read2line){
-        die("\nERROR: read1 and read2 export files do not contain the same number of reads.\n  Extra reads observed in read1 file at line no: $export_line_count.\n\n");
-      }
-      &export2sam_aux($read2line, $export_line_count, \@s2, \@conv_table, $is_paired, 2, $is_nofilter);
-
-      if (@s1 && @s2) { # then set mate coordinate
-        if($s1[SAM_QNAME] ne $s2[SAM_QNAME]){
-          die("\nERROR: Non-paired reads in export files on line: $export_line_count.\n  Read1: $_  Read2: $read2line\n");
-        }
-
-        my $isize = 0;
-        if ($s1[SAM_RNAME] ne '*' && $s1[SAM_RNAME] eq $s2[SAM_RNAME]) { # then calculate $isize
-          my $x1 = ($s1[SAM_FLAG] & 0x10)? $s1[SAM_POS] + length($s1[SAM_SEQ]) : $s1[SAM_POS];
-          my $x2 = ($s2[SAM_FLAG] & 0x10)? $s2[SAM_POS] + length($s2[SAM_SEQ]) : $s2[SAM_POS];
-          $isize = $x2 - $x1;
-        }
-
-        foreach ([\@s1,\@s2,$isize],[\@s2,\@s1,-$isize]){ 
-          my ($sa,$sb,$is) = @{$_};
-          if ($sb->[SAM_RNAME] ne '*') {
-            $sa->[SAM_MRNM] = ($sb->[SAM_RNAME] eq $sa->[SAM_RNAME]) ? "=" : $sb->[SAM_RNAME];
-            $sa->[SAM_MPOS] = $sb->[SAM_POS];
-            $sa->[SAM_ISIZE] = $is;
-            $sa->[SAM_FLAG] |= 0x20 if ($sb->[SAM_FLAG] & 0x10);
-          } else {
-            $sa->[SAM_FLAG] |= 0x8;
-          }
-        } 
-      }
-    }
-    print join("\t", @s1), "\n" if (@s1);
-    print join("\t", @s2), "\n" if (@s2 && $is_paired);
-  }
-  close($fh1);
-  if($is_paired) {
-    while(my $read2line = <$fh2>){
-      $export_line_count++;
-      die("\nERROR: read1 and read2 export files do not contain the same number of reads.\n  Extra reads observed in read2 file at line no: $export_line_count.\n\n");
-    }
-    close($fh2);
-  }
-}
-
-sub export2sam_aux {
-  my ($line, $line_no, $s, $ct, $is_paired, $read_no, $is_nofilter) = @_;
-  chomp($line);
-  my @t = split(/\t/, $line, -1);
-  my $isPassFilt = 1;
-  # Sorted files do not have passfilter column, so the number of columns can be total-1.
-  if(scalar(@t) < (EXPORT_SIZE - 1)) {
-    my $msg="\nERROR: Unexpected number of fields in export record on line $line_no of read$read_no export file. Found " . scalar(@t) . " fields but expected " . (EXPORT_SIZE - 1) . ".\n";
-    $msg.="\t...erroneous export record:\n" . $line . "\n\n";
-    die($msg);
-  }
-  elsif(scalar(@t) == EXPORT_SIZE) {
-    $isPassFilt = ($t[EXPORT_PASSFILT] eq 'Y');
-    return if(not ($isPassFilt or $is_nofilter));
-  }
-  @$s = ();
-  # read name
-  my $samQnamePrefix = $t[EXPORT_MACHINE] . (($t[EXPORT_RUNNO] ne "") ? "_" .  int($t[EXPORT_RUNNO]) : "");
-  $s->[SAM_QNAME] = join(':', $samQnamePrefix, int($t[EXPORT_LANE]), int($t[EXPORT_TILE]),
-                         int($t[EXPORT_X]), int($t[EXPORT_Y]));
-  # initial flag (will be updated later)
-  $s->[SAM_FLAG] = 0;
-  if($is_paired) {
-    if($t[EXPORT_READNO] != $read_no){
-      die("\nERROR: read$read_no export file contains record with read number: " .$t[EXPORT_READNO] . " on line: $line_no\n\n");
-    }
-    $s->[SAM_FLAG] |= 1 | 1<<(5 + $read_no);
-  }
-  $s->[SAM_FLAG] |= 0x200 if (not $isPassFilt);
-
-  # read & quality
-  my $is_export_rev = ($t[EXPORT_STRAND] eq 'R');
-  if ($is_export_rev) { # then reverse the sequence and quality
-    $s->[SAM_SEQ] = reverse($t[EXPORT_READ]);
-    $s->[SAM_SEQ] =~ tr/ACGTacgt/TGCAtgca/;
-    $s->[SAM_QUAL] = reverse($t[EXPORT_QUAL]);
-  } else {
-    $s->[SAM_SEQ] = $t[EXPORT_READ];
-    $s->[SAM_QUAL] = $t[EXPORT_QUAL];
-  }
-  my @convqual = ();
-  foreach (unpack('C*', $s->[SAM_QUAL])){
-    my $val=$ct->[$_];
-    if(not defined $val){
-      my $msg="\nERROR: can't interpret export quality value: " . $_ . " in read$read_no export file, line: $line_no\n";
-      if( $_ < 64 ) { $msg .= "  Use --qlogodds flag to translate logodds (solexa) quality values.\n"; }
-      die($msg . "\n");
-    }
-    push @convqual,$val;
-  }
-
-  $s->[SAM_QUAL] = pack('C*',@convqual); # change coding
-
-
-  # coor
-  my $has_coor = 0;
-  $s->[SAM_RNAME] = "*";
-  if (($t[EXPORT_CHROM] eq 'NM') or
-      ($t[EXPORT_CHROM] eq 'QC') or
-      ($t[EXPORT_CHROM] eq 'RM') or
-      ($t[EXPORT_CHROM] eq 'CONTROL')) {
-    $s->[SAM_FLAG] |= 0x4; # unmapped
-    push(@$s,"XC:Z:".$t[EXPORT_CHROM]) if($t[EXPORT_CHROM] ne 'NM');
-  } elsif ($t[EXPORT_CHROM] =~ /(\d+):(\d+):(\d+)/) {
-    $s->[SAM_FLAG] |= 0x4; # TODO: should I set BAM_FUNMAP in this case?
-    push(@$s, "H0:i:$1", "H1:i:$2", "H2:i:$3")
-  } elsif ($t[EXPORT_POS] < 1) {
-    $s->[SAM_FLAG] |= 0x4; # unmapped
-  } else {
-    $s->[SAM_RNAME] = $t[EXPORT_CHROM];
-    $s->[SAM_RNAME] .= "/" . $t[EXPORT_CONTIG] if($t[EXPORT_CONTIG] ne '');
-    $has_coor = 1;
-  }
-  $s->[SAM_POS] = $has_coor? $t[EXPORT_POS] : 0;
-
-#  print STDERR "t[14] = " . $t[14] . "\n";
-  my $matchDesc = '';
-  $s->[SAM_CIGAR] = "*";
-  if($has_coor){
-    $matchDesc = ($is_export_rev) ? reverse_compl_match_descriptor($t[EXPORT_MD]) : $t[EXPORT_MD];
-
-    if($matchDesc =~ /\^/){
-      # construct CIGAR string using Richard's function
-      $s->[SAM_CIGAR] = match_desc_to_cigar($matchDesc); # indel processing
-    } else {
-      $s->[SAM_CIGAR] = length($s->[SAM_SEQ]) . "M";
-    }
-  }
-
-#  print STDERR "cigar_string = $cigar_string\n";
-
-  $s->[SAM_FLAG] |= 0x10 if ($has_coor && $is_export_rev);
-  if($has_coor){
-    my $semap = ($t[EXPORT_SEMAP] ne '') ? $t[EXPORT_SEMAP] : 0;
-    my $pemap = 0;
-    if($is_paired) {
-      $pemap = ($t[EXPORT_PEMAP] ne '') ? $t[EXPORT_PEMAP] : 0;
-
-      # set `proper pair' bit if non-blank, non-zero PE alignment score:
-      $s->[SAM_FLAG] |= 0x02 if ($pemap > 0);
-    }
-    $s->[SAM_MAPQ] = min(254,max($semap,$pemap));
-  } else {
-    $s->[SAM_MAPQ] = 0;
-  }
-  # mate coordinate
-  $s->[SAM_MRNM] = '*';
-  $s->[SAM_MPOS] = 0;
-  $s->[SAM_ISIZE] = 0;
-  # aux
-  push(@$s, "BC:Z:$t[EXPORT_INDEX]") if ($t[EXPORT_INDEX]);
-  if($has_coor){
-    # The export match descriptor differs slightly from the samtools match descriptor.
-    # In order for the converted SAM files to be as compliant as possible,
-    # we put the export match descriptor in optional field 'XD' rather than 'MD':
-    push(@$s, "XD:Z:$matchDesc");
-    push(@$s, "SM:i:$t[EXPORT_SEMAP]") if ($t[EXPORT_SEMAP] ne '');
-    push(@$s, "AS:i:$t[EXPORT_PEMAP]") if ($is_paired and ($t[EXPORT_PEMAP] ne ''));
-  }
-}
-
-
-
-#
-# the following code is taken from Richard Shaw's sorted2sam.pl file
-#
-sub reverse_compl_match_descriptor($)
-{
-#    print "\nREVERSING THE MATCH DESCRIPTOR!\n";
-    my ($match_desc) = @_;
-    my $rev_compl_match_desc = reverse($match_desc);
-    $rev_compl_match_desc =~ tr/ACGT\^\$/TGCA\$\^/;
-
-    # Unreverse the digits of numbers.
-    $rev_compl_match_desc = join('',
-                                 map {($_ =~ /\d+/)
-                                      ? join('', reverse(split('', $_)))
-                                      : $_} split(/(\d+)/,
-                                                  $rev_compl_match_desc));
-
-    return $rev_compl_match_desc;
-}
-
-
-
-sub match_desc_to_cigar($)
-{
-    my ($match_desc) = @_;
-
-    my @match_desc_parts = split(/(\^.*?\$)/, $match_desc);
-    my $cigar_str = '';
-    my $cigar_del_ch = 'D';
-    my $cigar_ins_ch = 'I';
-    my $cigar_match_ch = 'M';
-
-    foreach my $match_desc_part (@match_desc_parts) {
-        next if (!$match_desc_part);
-
-        if ($match_desc_part =~ /^\^([ACGTN]+)\$$/) {
-            # Deletion
-            $cigar_str .= (length($1) . $cigar_del_ch);
-        } elsif ($match_desc_part =~ /^\^(\d+)\$$/) {
-            # Insertion
-            $cigar_str .= ($1 . $cigar_ins_ch);
-        } else {
-            $cigar_str .= (match_desc_frag_length($match_desc_part)
-                           . $cigar_match_ch);
-        }
-    }
-
-    return $cigar_str;
-}
-
-
-#------------------------------------------------------------------------------
-
-sub match_desc_frag_length($)
-                           {
-    my ($match_desc_str) = @_;
-    my $len = 0;
-
-    my @match_desc_fields = split(/([ACGTN]+)/, $match_desc_str);
-
-    foreach my $match_desc_field (@match_desc_fields) {
-        next if ($match_desc_field eq '');
-
-        $len += (($match_desc_field =~ /(\d+)/)
-                 ? $1 : length($match_desc_field));
-    }
-
-    return $len;
-}
-
-
-# argument holds the command line
-sub write_header($;$;$) 
-{
-	my ($progname,$version,$cl) = @_;
-	my $complete_header = "";
-	$complete_header .= "\@PG\tID:$progname\tVN:$version\tCL:$cl\n";
-
-	return $complete_header;
-}
diff -r 4ebcbb691426 -r b500f5f3c988 export2sam/illumina_export2sam_gz.pl
--- a/export2sam/illumina_export2sam_gz.pl	Fri Sep 12 02:42:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,562 +0,0 @@
-#!/usr/bin/env perl
-#
-#
-# illumina_export2sam.pl converts GERALD export files to SAM format.
-#
-#
-#
-########## License:
-#
-# The MIT License
-#
-# Original SAMtools work copyright (c) 2008-2009 Genome Research Ltd.
-# Modified SAMtools work copyright (c) 2010 Illumina, Inc.
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-# 
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-#
-#
-########## Additional notice for CASAVA installation:
-#
-# This file [illumina_export2sam.pl] in the CASAVA installation has
-# been copied from the file [export2sam.pl] in the SAMtools package
-# and modified by Illumina as permitted under the MIT license that
-# governs SAMtools. Illumina recommends the use of the modified
-# version to convert data from the Illumina export format to the SAM
-# file format. The terms of the MIT license specify your right to
-# further modify and distribute the SAMtools code. For the avoidance
-# of doubt, your rights with respect to copying, modifying, using and
-# distributing CASAVA are more restricted than the rights in the MIT
-# license, and are set forth in the Illumina Genome Analyzer Software
-# License Agreement and the Illumina Source Code License Agreement.
-#
-########## ChangeLog:
-#
-# Version: 2.3.1 (18MAR2011)
-#
-#   - Restore file '-' as stdin input.
-#
-# Version: 2.3.0 (24JAN2011)
-#
-#   - Add support for export reserved chromosome name "CONTROL",
-#       which is translated to optional field "XC:Z:CONTROL".
-#   - Check for ".gz" file extension on export files and open
-#       these as gzip pipes when the extension is found.
-#
-# Version: 2.2.0 (16NOV2010)
-#
-#   - Remove any leading zeros in export fields: RUNNO,LANE,TILE,X,Y
-#   - For export records with reserved chromosome name identifiers
-#       "QC" and "RM", add the optional field "XC:Z:QC" or "XC:Z:RM"
-#       to the SAM record, so that these cases can be distinguished
-#       from other unmatched reads.
-#
-# Version: 2.1.0 (21SEP2010)
-#
-#   - Additional export record error checking.
-#   - Convert export records with chromosome value of "RM" to unmapped
-#       SAM records.
-#
-# Version: 2.0.0 (15FEB2010)
-#
-#   Script updated by Illumina in conjunction with CASAVA 1.7.0
-#   release.
-#
-#   Major changes are as follows:
-#   - The CIGAR string has been updated to include all gaps from
-#       ELANDv2 alignments.
-#   - The ELAND single read alignment score is always stored in the
-#       optional "SM" field and the ELAND paired read alignment score
-#       is stored in the optional "AS" field when it exists.
-#   - The MAPQ value is set to the higher of the two alignment scores,
-#       but no greater than 254, i.e. min(254,max(SM,AS))
-#   - The SAM "proper pair" bit (0x0002) is now set for read pairs
-#       meeting ELAND's expected orientation and insert size criteria.
-#   - The default quality score translation is set for export files
-#       which contain Phread+64 quality values. An option,
-#       "--qlogodds", has been added to translate quality values from
-#       the Solexa+64 format used in export files prior to Pipeline
-#       1.3
-#   - The export match descriptor is now reverse-complemented when
-#       necessary such that it always corresponds to the forward
-#       strand of the reference, to be consistent with other
-#       information in the SAM record. It is now written to the
-#       optional 'XD' field (rather than 'MD') to acknowledge its
-#       minor differences from the samtools match descriptor (see
-#       additional detail below).
-#   - An option, "--nofilter", has been added to include reads which
-#       have failed primary analysis quality filtration. Such reads
-#       will have the corresponding SAM flag bit (0x0200) set.
-#   - Labels in the export 'contig' field are preserved by setting
-#       RNAME to "$export_chromosome/$export_contig" when the contig
-#       label exists.
-#
-#
-# Contact: lh3
-# Version: 0.1.2 (03JAN2009)
-#
-#
-#
-########## Known Conversion Limitations:
-#
-# - Export records for reads that map to a position < 1 (allowed
-#     in export format), are converted to unmapped reads in the SAM
-#     record.
-# - Export records contain the reserved chromosome names: "NM",
-#     "QC","RM" and "CONTROL". "NM" indicates that the aligner could
-#     not map the read to the reference sequence set. "QC" means that
-#     the aligner did not attempt to map the read due to some
-#     technical limitation. "RM" means that the read mapped to a set
-#     of 'contaminant' sequences specified in GERALD's RNA-seq
-#     workflow. "CONTROL" means that the read is a control. All of
-#     these alignment types are collapsed to the single unmapped
-#     alignment state in the SAM record, but the optional SAM "XC"
-#     field is used to record the original reserved chromosome name of
-#     the read for all but the "NM" case.
-# - The export match descriptor is slightly different than the
-#     samtools match descriptor. For this reason it is stored in the
-#     optional SAM field 'XD' (and not 'MD'). Note that the export
-#     match descriptor differs from the samtools version in two
-#     respects: (1) indels are explicitly closed with the '$'
-#     character and (2) insertions must be enumerated in the match
-#     descriptor. For example a 35-base read with a two-base insertion
-#     is described as: 20^2$14
-#
-#
-#
-
-my $version = "2.3.1";
-
-use strict;
-use warnings;
-
-use Getopt::Long;
-use File::Spec;
-use List::Util qw(min max);
-
-
-use constant {
-  EXPORT_MACHINE => 0,
-  EXPORT_RUNNO => 1,
-  EXPORT_LANE => 2,
-  EXPORT_TILE => 3,
-  EXPORT_X => 4,
-  EXPORT_Y => 5,
-  EXPORT_INDEX => 6,
-  EXPORT_READNO => 7,
-  EXPORT_READ => 8,
-  EXPORT_QUAL => 9,
-  EXPORT_CHROM => 10,
-  EXPORT_CONTIG => 11,
-  EXPORT_POS => 12,
-  EXPORT_STRAND => 13, 
-  EXPORT_MD => 14,
-  EXPORT_SEMAP => 15,
-  EXPORT_PEMAP => 16,
-  EXPORT_PASSFILT => 21,
-  EXPORT_SIZE => 22,
-};
-
-
-use constant {
-  SAM_QNAME => 0,
-  SAM_FLAG => 1,
-  SAM_RNAME => 2,
-  SAM_POS => 3,
-  SAM_MAPQ => 4,
-  SAM_CIGAR => 5,
-  SAM_MRNM => 6,
-  SAM_MPOS => 7,
-  SAM_ISIZE => 8,
-  SAM_SEQ => 9,
-  SAM_QUAL => 10,
-};
-
-
-# function prototypes for Richard's code
-sub match_desc_to_cigar($);
-sub match_desc_frag_length($);
-sub reverse_compl_match_descriptor($);
-sub write_header($;$;$);
-
-
-&export2sam;
-exit;
-
-
-
-
-sub export2sam {
-
-  my $cmdline = $0 . " " . join(" ",@ARGV);
-  my $arg_count = scalar @ARGV;
-  my $progname = "illumina_export2sam.pl";
-
-  my $is_logodds_qvals = 0; # if true, assume files contain logodds (i.e. "solexa") quality values
-  my $is_nofilter = 0;
-  my $read1file;
-  my $read2file;
-  my $print_version = 0;
-  my $help = 0;
-
-  my $result = GetOptions( "qlogodds" => \$is_logodds_qvals, 
-                           "nofilter" => \$is_nofilter,
-                           "read1=s"  => \$read1file,
-                           "read2=s"  => \$read2file,
-                           "version"  => \$print_version,
-                           "help"     => \$help );
-
-  my $usage = <<END;
-
-$progname converts GERALD export files to SAM format.
-
-Usage: $progname --read1=FILENAME [ options ] | --version | --help
-
-  --read1=FILENAME  read1 export file or '-' for stdin (mandatory)
-                      (file may be gzipped with ".gz" extension)
-  --read2=FILENAME  read2 export file or '-' for stdin
-                      (file may be gzipped with ".gz" extension)
-  --nofilter        include reads that failed the basecaller
-                      purity filter
-  --qlogodds        assume export file(s) use logodds quality values
-                      as reported by OLB (Pipeline) prior to v1.3
-                      (default: phred quality values)
-
-END
-
-  my $version_msg = <<END;
-
-$progname version: $version
-
-END
-
-  if((not $result) or $help or ($arg_count==0)) {
-    die($usage);
-  }
-
-  if(@ARGV) {
-    print STDERR "\nERROR: Unrecognized arguments: " . join(" ",@ARGV) . "\n\n";
-    die($usage);
-  }
-
-  if($print_version) {
-    die($version_msg);
-  }
-
-  if(not defined($read1file)) {
-    print STDERR "\nERROR: read1 export file must be specified\n\n";
-    die($usage);
-  }
-
-  unless((-f $read1file) or ($read1file eq '-')) {
-    die("\nERROR: Can't find read1 export file: '$read1file'\n\n");
-  }
-
-  if (defined $read2file) {
-    unless((-f $read2file) or ($read2file eq '-')) {
-      die("\nERROR: Can't find read2 export file: '$read2file'\n\n");
-    }
-    if($read1file eq $read2file) {
-      die("\nERROR: read1 and read2 export filenames are the same: '$read1file'\n\n");
-    }
-  }
-
-  my ($fh1, $fh2, $is_paired);
-
-  my $read1cmd="$read1file";
-  $read1cmd = "gzip -dc $read1file |";
-  open($fh1, $read1cmd)
-      or die("\nERROR: Can't open read1 process: '$read1cmd'\n\n");
-  $is_paired = defined $read2file;
-  if ($is_paired) {
-    my $read2cmd="$read2file";
-    $read2cmd = "gzip -dc $read2file |";
-    open($fh2, $read2cmd)
-        or die("\nERROR: Can't open read2 process: '$read2cmd'\n\n");
-  }
-  # quality value conversion table
-  my @conv_table;
-  if($is_logodds_qvals){ # convert from solexa+64 quality values (pipeline pre-v1.3):
-    for (-64..64) {
-      $conv_table[$_+64] = int(33 + 10*log(1+10**($_/10.0))/log(10)+.499);
-    }
-  } else {               # convert from phred+64 quality values (pipeline v1.3+):
-    for (-64..-1) {
-      $conv_table[$_+64] = undef;
-    }
-    for (0..64) {
-      $conv_table[$_+64] = int(33 + $_);
-    }
-  }
-  # write the header
-  print write_header( $progname, $version, $cmdline );
-  # core loop
-  my $export_line_count = 0;
-  while (<$fh1>) {
-    $export_line_count++;
-    my (@s1, @s2);
-    &export2sam_aux($_, $export_line_count, \@s1, \@conv_table, $is_paired, 1, $is_nofilter);
-    if ($is_paired) {
-      my $read2line = <$fh2>;
-      if(not $read2line){
-        die("\nERROR: read1 and read2 export files do not contain the same number of reads.\n  Extra reads observed in read1 file at line no: $export_line_count.\n\n");
-      }
-      &export2sam_aux($read2line, $export_line_count, \@s2, \@conv_table, $is_paired, 2, $is_nofilter);
-
-      if (@s1 && @s2) { # then set mate coordinate
-        if($s1[SAM_QNAME] ne $s2[SAM_QNAME]){
-          die("\nERROR: Non-paired reads in export files on line: $export_line_count.\n  Read1: $_  Read2: $read2line\n");
-        }
-
-        my $isize = 0;
-        if ($s1[SAM_RNAME] ne '*' && $s1[SAM_RNAME] eq $s2[SAM_RNAME]) { # then calculate $isize
-          my $x1 = ($s1[SAM_FLAG] & 0x10)? $s1[SAM_POS] + length($s1[SAM_SEQ]) : $s1[SAM_POS];
-          my $x2 = ($s2[SAM_FLAG] & 0x10)? $s2[SAM_POS] + length($s2[SAM_SEQ]) : $s2[SAM_POS];
-          $isize = $x2 - $x1;
-        }
-
-        foreach ([\@s1,\@s2,$isize],[\@s2,\@s1,-$isize]){ 
-          my ($sa,$sb,$is) = @{$_};
-          if ($sb->[SAM_RNAME] ne '*') {
-            $sa->[SAM_MRNM] = ($sb->[SAM_RNAME] eq $sa->[SAM_RNAME]) ? "=" : $sb->[SAM_RNAME];
-            $sa->[SAM_MPOS] = $sb->[SAM_POS];
-            $sa->[SAM_ISIZE] = $is;
-            $sa->[SAM_FLAG] |= 0x20 if ($sb->[SAM_FLAG] & 0x10);
-          } else {
-            $sa->[SAM_FLAG] |= 0x8;
-          }
-        } 
-      }
-    }
-    print join("\t", @s1), "\n" if (@s1);
-    print join("\t", @s2), "\n" if (@s2 && $is_paired);
-  }
-  close($fh1);
-  if($is_paired) {
-    while(my $read2line = <$fh2>){
-      $export_line_count++;
-      die("\nERROR: read1 and read2 export files do not contain the same number of reads.\n  Extra reads observed in read2 file at line no: $export_line_count.\n\n");
-    }
-    close($fh2);
-  }
-}
-
-sub export2sam_aux {
-  my ($line, $line_no, $s, $ct, $is_paired, $read_no, $is_nofilter) = @_;
-  chomp($line);
-  my @t = split(/\t/, $line, -1);
-  my $isPassFilt = 1;
-  # Sorted files do not have passfilter column, so the number of columns can be total-1.
-  if(scalar(@t) < (EXPORT_SIZE - 1)) {
-    my $msg="\nERROR: Unexpected number of fields in export record on line $line_no of read$read_no export file. Found " . scalar(@t) . " fields but expected " . (EXPORT_SIZE - 1) . ".\n";
-    $msg.="\t...erroneous export record:\n" . $line . "\n\n";
-    die($msg);
-  }
-  elsif(scalar(@t) == EXPORT_SIZE) {
-    $isPassFilt = ($t[EXPORT_PASSFILT] eq 'Y');
-    return if(not ($isPassFilt or $is_nofilter));
-  }
-  @$s = ();
-  # read name
-  my $samQnamePrefix = $t[EXPORT_MACHINE] . (($t[EXPORT_RUNNO] ne "") ? "_" .  int($t[EXPORT_RUNNO]) : "");
-  $s->[SAM_QNAME] = join(':', $samQnamePrefix, int($t[EXPORT_LANE]), int($t[EXPORT_TILE]),
-                         int($t[EXPORT_X]), int($t[EXPORT_Y]));
-  # initial flag (will be updated later)
-  $s->[SAM_FLAG] = 0;
-  if($is_paired) {
-    if($t[EXPORT_READNO] != $read_no){
-      die("\nERROR: read$read_no export file contains record with read number: " .$t[EXPORT_READNO] . " on line: $line_no\n\n");
-    }
-    $s->[SAM_FLAG] |= 1 | 1<<(5 + $read_no);
-  }
-  $s->[SAM_FLAG] |= 0x200 if (not $isPassFilt);
-
-  # read & quality
-  my $is_export_rev = ($t[EXPORT_STRAND] eq 'R');
-  if ($is_export_rev) { # then reverse the sequence and quality
-    $s->[SAM_SEQ] = reverse($t[EXPORT_READ]);
-    $s->[SAM_SEQ] =~ tr/ACGTacgt/TGCAtgca/;
-    $s->[SAM_QUAL] = reverse($t[EXPORT_QUAL]);
-  } else {
-    $s->[SAM_SEQ] = $t[EXPORT_READ];
-    $s->[SAM_QUAL] = $t[EXPORT_QUAL];
-  }
-  my @convqual = ();
-  foreach (unpack('C*', $s->[SAM_QUAL])){
-    my $val=$ct->[$_];
-    if(not defined $val){
-      my $msg="\nERROR: can't interpret export quality value: " . $_ . " in read$read_no export file, line: $line_no\n";
-      if( $_ < 64 ) { $msg .= "  Use --qlogodds flag to translate logodds (solexa) quality values.\n"; }
-      die($msg . "\n");
-    }
-    push @convqual,$val;
-  }
-
-  $s->[SAM_QUAL] = pack('C*',@convqual); # change coding
-
-
-  # coor
-  my $has_coor = 0;
-  $s->[SAM_RNAME] = "*";
-  if (($t[EXPORT_CHROM] eq 'NM') or
-      ($t[EXPORT_CHROM] eq 'QC') or
-      ($t[EXPORT_CHROM] eq 'RM') or
-      ($t[EXPORT_CHROM] eq 'CONTROL')) {
-    $s->[SAM_FLAG] |= 0x4; # unmapped
-    push(@$s,"XC:Z:".$t[EXPORT_CHROM]) if($t[EXPORT_CHROM] ne 'NM');
-  } elsif ($t[EXPORT_CHROM] =~ /(\d+):(\d+):(\d+)/) {
-    $s->[SAM_FLAG] |= 0x4; # TODO: should I set BAM_FUNMAP in this case?
-    push(@$s, "H0:i:$1", "H1:i:$2", "H2:i:$3")
-  } elsif ($t[EXPORT_POS] < 1) {
-    $s->[SAM_FLAG] |= 0x4; # unmapped
-  } else {
-    $s->[SAM_RNAME] = $t[EXPORT_CHROM];
-    $s->[SAM_RNAME] .= "/" . $t[EXPORT_CONTIG] if($t[EXPORT_CONTIG] ne '');
-    $has_coor = 1;
-  }
-  $s->[SAM_POS] = $has_coor? $t[EXPORT_POS] : 0;
-
-#  print STDERR "t[14] = " . $t[14] . "\n";
-  my $matchDesc = '';
-  $s->[SAM_CIGAR] = "*";
-  if($has_coor){
-    $matchDesc = ($is_export_rev) ? reverse_compl_match_descriptor($t[EXPORT_MD]) : $t[EXPORT_MD];
-
-    if($matchDesc =~ /\^/){
-      # construct CIGAR string using Richard's function
-      $s->[SAM_CIGAR] = match_desc_to_cigar($matchDesc); # indel processing
-    } else {
-      $s->[SAM_CIGAR] = length($s->[SAM_SEQ]) . "M";
-    }
-  }
-
-#  print STDERR "cigar_string = $cigar_string\n";
-
-  $s->[SAM_FLAG] |= 0x10 if ($has_coor && $is_export_rev);
-  if($has_coor){
-    my $semap = ($t[EXPORT_SEMAP] ne '') ? $t[EXPORT_SEMAP] : 0;
-    my $pemap = 0;
-    if($is_paired) {
-      $pemap = ($t[EXPORT_PEMAP] ne '') ? $t[EXPORT_PEMAP] : 0;
-
-      # set `proper pair' bit if non-blank, non-zero PE alignment score:
-      $s->[SAM_FLAG] |= 0x02 if ($pemap > 0);
-    }
-    $s->[SAM_MAPQ] = min(254,max($semap,$pemap));
-  } else {
-    $s->[SAM_MAPQ] = 0;
-  }
-  # mate coordinate
-  $s->[SAM_MRNM] = '*';
-  $s->[SAM_MPOS] = 0;
-  $s->[SAM_ISIZE] = 0;
-  # aux
-  push(@$s, "BC:Z:$t[EXPORT_INDEX]") if ($t[EXPORT_INDEX]);
-  if($has_coor){
-    # The export match descriptor differs slightly from the samtools match descriptor.
-    # In order for the converted SAM files to be as compliant as possible,
-    # we put the export match descriptor in optional field 'XD' rather than 'MD':
-    push(@$s, "XD:Z:$matchDesc");
-    push(@$s, "SM:i:$t[EXPORT_SEMAP]") if ($t[EXPORT_SEMAP] ne '');
-    push(@$s, "AS:i:$t[EXPORT_PEMAP]") if ($is_paired and ($t[EXPORT_PEMAP] ne ''));
-  }
-}
-
-
-
-#
-# the following code is taken from Richard Shaw's sorted2sam.pl file
-#
-sub reverse_compl_match_descriptor($)
-{
-#    print "\nREVERSING THE MATCH DESCRIPTOR!\n";
-    my ($match_desc) = @_;
-    my $rev_compl_match_desc = reverse($match_desc);
-    $rev_compl_match_desc =~ tr/ACGT\^\$/TGCA\$\^/;
-
-    # Unreverse the digits of numbers.
-    $rev_compl_match_desc = join('',
-                                 map {($_ =~ /\d+/)
-                                      ? join('', reverse(split('', $_)))
-                                      : $_} split(/(\d+)/,
-                                                  $rev_compl_match_desc));
-
-    return $rev_compl_match_desc;
-}
-
-
-
-sub match_desc_to_cigar($)
-{
-    my ($match_desc) = @_;
-
-    my @match_desc_parts = split(/(\^.*?\$)/, $match_desc);
-    my $cigar_str = '';
-    my $cigar_del_ch = 'D';
-    my $cigar_ins_ch = 'I';
-    my $cigar_match_ch = 'M';
-
-    foreach my $match_desc_part (@match_desc_parts) {
-        next if (!$match_desc_part);
-
-        if ($match_desc_part =~ /^\^([ACGTN]+)\$$/) {
-            # Deletion
-            $cigar_str .= (length($1) . $cigar_del_ch);
-        } elsif ($match_desc_part =~ /^\^(\d+)\$$/) {
-            # Insertion
-            $cigar_str .= ($1 . $cigar_ins_ch);
-        } else {
-            $cigar_str .= (match_desc_frag_length($match_desc_part)
-                           . $cigar_match_ch);
-        }
-    }
-
-    return $cigar_str;
-}
-
-
-#------------------------------------------------------------------------------
-
-sub match_desc_frag_length($)
-                           {
-    my ($match_desc_str) = @_;
-    my $len = 0;
-
-    my @match_desc_fields = split(/([ACGTN]+)/, $match_desc_str);
-
-    foreach my $match_desc_field (@match_desc_fields) {
-        next if ($match_desc_field eq '');
-
-        $len += (($match_desc_field =~ /(\d+)/)
-                 ? $1 : length($match_desc_field));
-    }
-
-    return $len;
-}
-
-
-# argument holds the command line
-sub write_header($;$;$) 
-{
-	my ($progname,$version,$cl) = @_;
-	my $complete_header = "";
-	$complete_header .= "\@PG\tID:$progname\tVN:$version\tCL:$cl\n";
-
-	return $complete_header;
-}