Mercurial > repos > jdv > b2b_bam2consensus

annotate sync_reads @ 1:2367d00c5182 draft default tip

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author jdv
date Tue, 28 Sep 2021 06:12:40 +0000
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2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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1 #!/usr/bin/env perl
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3 use strict;
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4 use warnings;
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5 use 5.012;
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6
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7 use autodie qw/open close/;
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8 use BioX::Seq::Stream;
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9 use Getopt::Long;
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10 use Pod::Usage;
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11
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12 my $reads1;
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13 my $reads2;
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14 my $singles;
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15 my $sync_suffix = 'sync';
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16 my $singles_suffix = 'singles';
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17 my $compress = ''; # one of 'gzip' or 'dsrc'
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18 my $outname1;
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19 my $outname2;
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20 my $singles1_name;
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21 my $singles2_name;
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22
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23 use constant DSRC_BIN => 'dsrc';
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24 use constant GZIP_BIN => 'gzip';
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25 use constant NAME => 'sync_reads';
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26 use constant VERSION => '0.005';
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27
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28 GetOptions(
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29
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30 'fwd=s' => \$reads1,
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31 'rev=s' => \$reads2,
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32 'singles' => \$singles,
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33 'fwd_out=s' => \$outname1,
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34 'rev_out=s' => \$outname2,
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35 'fwd_singles_out=s' => \$singles1_name,
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36 'rev_singles_out=s' => \$singles2_name,
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37 'sync_suffix=s' => \$sync_suffix,
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38 'singles_suffix=s' => \$singles_suffix,
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39 'compress:s' => \$compress,
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40 'help' => sub{ pod2usage(-verbose => 2); },
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41 'version' => sub{ print 'This is ', NAME, ' v', VERSION, "\n";exit; },
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42
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43 ) or pod2usage( -verbose => 1 );
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44
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45 pod2usage(-verbose => 1, -msg => "Error: input files can\'t be read")
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46 if (! -r $reads1 || ! -r $reads2);
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47
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48 # open output filehandles, possibly with compression
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49 if (! defined $outname1) {
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50 $outname1 = $reads1;
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51 $outname1 =~ s/([^\.]+)$/$sync_suffix\.$1/;
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52 }
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53 if (! defined $outname2) {
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54 $outname2 = $reads2;
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55 $outname2 =~ s/([^\.]+)$/$sync_suffix\.$1/;
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56 }
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57 my $mode = $compress =~ /^(?:gzip|dsrc)$/ ? '|-' : '>';
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58 my $cmd = $compress eq 'gzip' ? GZIP_BIN . ' -c > '
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59 : $compress eq 'dsrc' ? DSRC_BIN . ' c -m2 -s '
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60 : '';
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61 my $suffix = $compress eq 'gzip' ? '.gz'
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62 : $compress eq 'dsrc' ? '.dsrc'
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63 : '';
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64 open my $s1, $mode, $cmd . $outname1 . $suffix;
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65 open my $s2, $mode, $cmd . $outname2 . $suffix;
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66
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67
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68 # open singles output filehandles if requested, possibly with compression
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69 my $up1;
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70 my $up2;
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71 if ($singles) {
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72 if (! defined $singles1_name) {
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73 $singles1_name = $reads1;
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74 $singles1_name =~ s/([^\.]+)$/$singles_suffix\.$1/;
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75 }
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76 if (! defined $singles2_name) {
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77 $singles2_name = $reads2;
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78 $singles2_name =~ s/([^\.]+)$/$singles_suffix\.$1/;
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79 }
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80 $mode = $compress =~ /^(?:gzip|dsrc)$/ ? '|-' : '>';
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81 $cmd = $compress eq 'gzip' ? GZIP_BIN . ' -c > '
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82 : $compress eq 'dsrc' ? DSRC_BIN . ' c -m2 -s '
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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83 : '';
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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84 my $suffix = $compress eq 'gzip' ? '.gz'
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
85 : $compress eq 'dsrc' ? '.dsrc'
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
86 : '';
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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87 open $up1, $mode, $cmd . $singles1_name . $suffix;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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88 open $up2, $mode, $cmd . $singles2_name . $suffix;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
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89 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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90
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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91 my $ll_f1 = {};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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92 my $ll_f2 = {};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
93 my $f1_prev;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
94 my $f2_prev;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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95 my $f1_open = 1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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96 my $f2_open = 1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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97
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
98 my $parser1 = BioX::Seq::Stream->new($reads1);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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99 my $parser2 = BioX::Seq::Stream->new($reads2);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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100
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diff changeset
101 while ($f1_open || $f2_open) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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102
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103 # process next read for file 1
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104 if ($f1_open && defined (my $seq = $parser1->next_seq)) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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105 my $name = $seq->id;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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106 $name =~ s/\/[12]$//; #remove directional tag if present
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
107 if (defined $ll_f2->{$name}) {
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108 my $prev = $ll_f2->{$name}->{prev} // undef;
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109 purge_cache( $ll_f2, $prev, $up2 );
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
110 purge_cache( $ll_f1, $f1_prev, $up1 );
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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111 print {$s1} $seq->as_fastq;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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112 print {$s2} $ll_f2->{$name}->{read};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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113 delete $ll_f2->{$name};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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114 $f1_prev = undef;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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115 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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116 else {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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117 $ll_f1->{$name}->{read} = $seq->as_fastq;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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118 $ll_f1->{$name}->{prev} = $f1_prev // undef;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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119 $f1_prev = $name;
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120 }
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121 }
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122 else {
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123 $f1_open = 0;
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124 }
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125
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126 # process next read for file 2
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127 if ($f2_open && defined (my $seq = $parser2->next_seq)) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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128 my $name = $seq->id;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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129 $name =~ s/\/[12]$//; #remove directional tag if present
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130 if (defined $ll_f1->{$name}) {
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131 my $prev = $ll_f1->{$name}->{prev} // undef;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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132 purge_cache( $ll_f1, $prev, $up1 );
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
133 purge_cache( $ll_f2, $f2_prev, $up2 );
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134 print {$s2} $seq->as_fastq;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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135 print {$s1} $ll_f1->{$name}->{read};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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136 delete $ll_f1->{$name};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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137 $f2_prev = undef;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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138 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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139 else {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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140 $ll_f2->{$name}->{read} = $seq->as_fastq;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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141 $ll_f2->{$name}->{prev} = $f2_prev // undef;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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142 $f2_prev = $name;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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143 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
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144 }
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145 else {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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146 $f2_open = 0;
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147 }
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148 }
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149
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
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150 #handle remaining unpaired reads if necessary
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parents:
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151 if ($singles) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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152 purge_cache( $ll_f1, $f1_prev, $up1 );
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
153 purge_cache( $ll_f2, $f2_prev, $up2 );
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
154 close $up1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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155 close $up2;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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156 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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157
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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158 exit;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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159
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
160 sub purge_cache {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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161
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
162 my ($ll, $prev, $fh) = @_;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
163 while (defined $prev && defined $ll->{$prev}) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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164 my $prev2 = $ll->{$prev}->{prev} // undef;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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165 print {$fh} $ll->{$prev}->{read} if ($singles);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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166 delete $ll->{$prev};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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167 $prev = $prev2;
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168 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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169
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170 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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171
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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172
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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173 __END__
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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174
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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175 =head1 NAME
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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176
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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177 sync_reads - resynchronize paired FASTQ files
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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178
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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179 =head1 SYNOPSIS
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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180
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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181 sync_reads [options] --fwd I<left_reads> --rev I<right reads>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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182
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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183 =head1 DESCRIPTION
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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184
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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185 B<sync_reads> will re-synchronize two FASTQ files containing paired reads which
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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186 are no longer in sync due to individual removal of reads during pre-processing
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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187 (trimming, filtering, etc). In this case, "in sync" means that both files have
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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188 the same number of reads and, at any given read position in the files, the
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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189 corresponding reads represent proper pairs. The resulting files will contain
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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190 matching reads in order (assuming the input files were properly ordered). It
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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191 will optionally print out unpaired reads to separate files. Memory usage is
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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192 not dependent on the input file size but rather the maximum distance between
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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193 paired reads in the two files, as the read cache is flushed each time paired
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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194 reads are identified. In the worst-case scenario (one file has a single read
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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195 that pairs with the last read in the matching file) memory usage can approach
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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196 the largest file size, but in typical usage it rarely exceeds a few MB
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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197 regardless of file size.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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198
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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199 B<IMPORTANT:> Reads in input files MUST be in the same order, aside from
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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200 missing reads, or the output will report many valid pairs as singletons.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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201
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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202 =head1 OPTIONS
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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203
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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204 =head2 Mandatory
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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205
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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206 =over 4
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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207
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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208 =item B<--fwd> I<forward_fastq>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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209
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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210 Specify FASTQ file containing the first of the trimmed read pairs
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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211
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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212 =item B<--rev> I<reverse_fastq>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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213
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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214 Specify FASTQ file containing the second of the trimmed read pairs
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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215
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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216 =back
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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217
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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218 =head2 Optional
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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219
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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220 =over 4
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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221
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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222 =item B<--fwd_out> I<filename>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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223
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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224 Specify output name for synced forward reads
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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225
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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226 =item B<--rev_out> I<filename>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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227
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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228 Specify output name for synced reverse reads
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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229
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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230 =item B<--fwd_singles_out> I<filename>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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231
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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232 Specify output name for forward singleton reads
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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233
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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234 =item B<--rev_singles_out> I<filename>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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235
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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236 Specify output name for reverse singleton reads
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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237
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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238 =item B<--sync_suffix> I<suffix>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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239
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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240 Specify suffix to add to synced read output files. This will be added to the
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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241 input read name before the final suffix (i.e. after the last period). Default
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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242 is 'sync'.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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243
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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244 =item B<--compress> I<gzip|dsrc>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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245
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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246 Specify type of compression for output files (will compress all output files)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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247
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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248 =item B<--singles>
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249
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250 If given, unpaired reads will be written to separate output files. Default is
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251 FALSE.
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252
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253 =item B<--singles_suffix> I<suffix>
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254
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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255 Specify suffix to add to singles read output files. This will be added to the
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256 input read name before the final suffix (i.e. after the last period). Default
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257 is 'singles'.
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258
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259 =item B<--help>
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260
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261 Display this usage page
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262
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263 =item B<--version>
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264
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265 Print version information
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266
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267 =back
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268
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269 =head1 CAVEATS AND BUGS
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270
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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271 Currently no input validation is performed on the input files. Files are
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272 assumed to be standard FASTQ file format with each read represented by four
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273 lines and no other extraneous information present. B<CRITICALLY>, they are also
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274 assumed to be in the same input order after accounting for deleted reads
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275 (the software will fail miserably if this is not the case).
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276
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277 Please submit bug reports to the issue tracker in the distribution repository.
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278
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279 =head1 AUTHOR
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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280
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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281 Jeremy Volkening <jdv@base2bio.com>
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282
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283 =head1 COPYRIGHT AND LICENSE
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284
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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285 Copyright 2014-16 Jeremy Volkening
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286
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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287 This program is free software: you can redistribute it and/or modify
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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288 it under the terms of the GNU General Public License as published by
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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289 the Free Software Foundation, either version 3 of the License, or
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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290 (at your option) any later version.
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291
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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292 This program is distributed in the hope that it will be useful,
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293 but WITHOUT ANY WARRANTY; without even the implied warranty of
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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294 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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295 GNU General Public License for more details.
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296
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297 You should have received a copy of the GNU General Public License
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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298 along with this program. If not, see <http://www.gnu.org/licenses/>.
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299
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300 =cut