Mercurial > repos > jdv > nanopolish

annotate nanopolish_variants.pl @ 2:e4b6d4a53f2e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author jdv
date Tue, 03 Oct 2017 21:23:56 -0400
parents 2136c2725fc4
children a1d433401bc2
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2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
parents:
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1 #!/usr/bin/env perl
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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2
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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3 use strict;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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4 use warnings;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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5 use 5.012;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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6
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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7 use Archive::Tar;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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8 use Cwd qw/getcwd abs_path/;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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9 use File::Copy qw/copy/;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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10 use Getopt::Long qw/:config pass_through/;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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11 use threads;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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12 use threads::shared;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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13 use BioX::Seq::Stream;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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14
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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15 my $fn_genome;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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16 my $threads = 1;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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17 my $fn_outfile;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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18 my $fn_consensus;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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19 my $fn_fast5;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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20
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21 # remember full command string (with proper binary)
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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22
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23 # parse genome filename and add back to arg stack
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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24 GetOptions(
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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25 'genome=s' => \$fn_genome,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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26 'threads=i' => \$threads,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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27 'outfile=s' => \$fn_outfile,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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28 'consensus=s' => \$fn_consensus,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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29 'fast5=s' => \$fn_fast5,
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30 );
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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31
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32 my $tmp_dir = 'tmp_dir';
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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33 mkdir $tmp_dir;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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34
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35 #extract FAST5 files to path where they are expected
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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36 my $in_dir = 'in_dir';
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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37 mkdir $in_dir;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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38 my $cwd = abs_path( getcwd() );
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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39 chdir $in_dir;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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40 my $tar = Archive::Tar->new();
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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41 $tar->read($fn_fast5);
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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42 $tar->extract();
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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43 chdir $cwd;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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44
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45 my @cmd = @ARGV;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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46 unshift @cmd, 'nanopolish';
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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47 push @cmd, '--genome', $fn_genome;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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48
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49 say join ' ', @cmd;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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50
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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51 my @regions :shared;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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52
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53 # build region tags to pass to nanopolish
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54 my $parser = BioX::Seq::Stream->new($fn_genome);
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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55 while (my $seq = $parser->next_seq) {
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56 push @regions, join( ':', $seq->id,
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57 join( '-', 1, length($seq) ),
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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58 );
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59 }
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60
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61 my @workers;
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62 for (1..$threads) {
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63 push @workers, threads->create(\&run);
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64 }
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65
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66 $_->join() for (@workers);
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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67
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68 my @fa_files = glob "$tmp_dir/*.fasta";
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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69 my @out_files = glob "$tmp_dir/*.vcf";
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70
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71 open my $out_cons, '>', $fn_consensus
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72 or die "Failed to open output consensus: $!";
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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73 for (@fa_files) {
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74 open my $in, '<', $_;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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75 while (my $line = <$in>) {
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76 print {$out_cons} $line;
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77 }
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78 close $in;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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79 }
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80 close $out_cons;
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81
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82 # we may need to do extra processing on VCF output
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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83 open my $out_vcf, '>', $fn_outfile
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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84 or die "Failed to open output file: $!";
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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85 for my $i (0..$#out_files) {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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86 my $v = $out_files[$i];
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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87 open my $in, '<', $v;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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88 while (my $line = <$in>) {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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89 next if ($line =~ /^\s*#/ && $i > 0);
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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90 print {$out_vcf} $line;
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91 }
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92 close $in;
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93 }
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94 close $out_vcf;
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95
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96
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97 sub run {
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98
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99 LOOP:
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100 while (1) {
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101
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102 my $tag;
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103
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104 {
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105 lock @regions;
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106 last LOOP if (! scalar @regions);
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107 $tag = shift @regions;
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108 }
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109
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110 my $fn_out = "$tmp_dir/$tag.vcf";
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111 my $fn_cons = "$tmp_dir/$tag.fasta";
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112
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113 my @cmd_local = @cmd;
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114 push @cmd_local, '--window', $tag;
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115 push @cmd_local, '--outfile', $fn_out;
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116 push @cmd_local, '--consensus', $fn_cons;
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117
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118 my $ret = system @cmd_local;
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119 warn "RET: $ret ($!)\n";
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120
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121 my $cmd_string = join ' ', @cmd_local;
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122 die "Non-zero exit value for command: $cmd_string\n"
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123 if ($ret);
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124
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125 }
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126
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127 }