Mercurial > repos > jvolkening > b2b_count_mapped_reads

annotate frag_lens @ 0:90d81e551420 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
author jvolkening
date Sat, 02 Mar 2024 07:42:45 +0000
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90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
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1 #!/usr/bin/env perl
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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2
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3 use strict;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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4 use warnings;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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5 use 5.012;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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6
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7 use Cwd qw/abs_path/;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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8 use File::Temp qw/tempdir tempfile/;
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9 use IPC::Cmd qw/can_run/;
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10 use List::Util qw/sum/;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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11 use Getopt::Long;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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12 use Pod::Usage;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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13
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14 my @good_codes = ( 0x0002, 0x0040 );
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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15 my @bad_codes = ( 0x0004, 0x0100, 0x0800 );
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16
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17 #-inputs---------------------------------------------------------------------#
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18 my $fasta;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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19 my $forward;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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20 my $reverse;
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21 my $sam;
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22 #-knobs----------------------------------------------------------------------#
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23 my $threads = 1;
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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24 my $max_align = 10000;
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25
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26 my $PROGRAM = 'frag_lens';
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27 my $VERSION = 0.001;
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28
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29 GetOptions(
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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30 #-inputs-----------------------------------------------------------------#
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31 'sam=s' => \$sam,
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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32 'forward=s' => \$forward,
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33 'reverse=s' => \$reverse,
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34 'ref=s' => \$fasta,
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35 #-knobs------------------------------------------------------------------#
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36 'threads=i' => \$threads,
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37 'max_aln=i' => \$max_align,
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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38 'help' => sub{ pod2usage(-verbose => 2); },
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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39 'version' => sub{ say "This is $PROGRAM v$VERSION";exit; },
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40
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41 ) or pod2usage( -verbose => 1);
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42
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43 my $fh_sam;
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44 my $tmp_fasta;
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45
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46 if (defined $sam) {
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47 open $fh_sam, '<', $sam or die "failed to open SAM\n";
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48 }
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49
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50 else {
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51
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52 my $BWA = can_run('bwa')
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53 // die "BWA is required but not found\n";
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54
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55 my ($tmp_dir) = tempdir( CLEANUP => 1);
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56
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57 die "specify forward and reverse read files and reference\n"
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58 if (! defined $forward || ! defined $reverse || ! defined $fasta);
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59
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60 $fasta = abs_path($fasta);
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61
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62 my $res = system(
90d81e551420 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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63 'ln',
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64 '-s',
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65 $fasta,
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66 "$tmp_dir/tmp.fasta"
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67 );
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68 die "link failed" if ($res);
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69 $res = system(
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70 $BWA,
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71 'index',
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72 "$tmp_dir/tmp.fasta"
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73 );
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74 die "index failed" if ($res);
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75 open $fh_sam, '-|', $BWA,
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76 'mem',
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77 '-t' => $threads,
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78 '-v' => 1,
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79 "$tmp_dir/tmp.fasta",
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80 $forward,
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81 $reverse
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82 ;
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83 }
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84
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85 my $c = 0;
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86 while (my $line = <$fh_sam>) {
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87 next if ($line =~ /^\@/);
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88 chomp $line;
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89 my @parts = split "\t", $line;
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90 my $flags = $parts[1];
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91 my $sum1 = sum map {$_ & $flags ? 1 : 0} @good_codes;
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92 my $sum2 = sum map {$_ & $flags ? 1 : 0} @bad_codes;
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93 if ($sum1 == scalar @good_codes && $sum2 == 0) {
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94 say abs($parts[8]);
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95 last if (++$c >= $max_align);
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96 }
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97 }
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98 close $fh_sam;
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99
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100 __END__
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101
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102 =head1 NAME
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103
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104 frag_lens - Calculate paired end fragment lengths from read alignment
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105
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106 =head1 SYNOPSIS
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107
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108 frag_lens [--sam <in.sam>] OR [--ref <cons.fa> --forward <R1.fq> --reverse <R2.fq>] [options] > frag_lens.txt
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109
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110 =head1 DESCRIPTION
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111
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112 Calculates library fragment lengths based on paired-end read alignment.
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113 Takes as input either a preprepared SAM alignment or a reference and read
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114 files from which it produces an alignment. Outputs calculated fragment
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115 lengths, one per line.
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116
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117 =head1 PREREQUISITES
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118
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119 Requires the following binaries:
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120
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121 =over 1
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122
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123 =item * bwa
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124
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125 =back
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126
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127 =head1 OPTIONS
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128
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129 =head2 Input option one
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130
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131 =over 4
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132
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133 =item B<--sam> I<filename>
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134
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135 Path to input SAM alignment.
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136
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137 =back
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138
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139 =head2 Input option two
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140
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141 =over 4
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142
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143 =item B<--ref> I<filename>
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144
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145 Path to reference sequence (e.g. assembly)
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146
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147 =item B<--forward> I<filename>
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148
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149 Forward reads in FASTQ format
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150
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151 =item B<--reverse> I<filename>
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152
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153 Reverse reads in FASTQ format
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154
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155 =back
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156
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157 =head2 Configuration
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158
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159 =over 4
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160
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161 =item B<--max_align>
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162
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163 Maximum number of alignment records to read as input. Used to limit run times.
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164
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165 =item B<--threads>
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166
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167 Number of threads to use for alignment (ignored if --sam is given)
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168
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169 =back
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170
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171 =head1 CAVEATS AND BUGS
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172
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173 Please submit bug reports to the issue tracker in the distribution repository.
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174
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175 =head1 AUTHOR
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176
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177 Jeremy Volkening (jdv@base2bio.com)
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178
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179 =head1 LICENSE AND COPYRIGHT
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180
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181 Copyright 2014-19 Jeremy Volkening
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182
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183 This program is free software: you can redistribute it and/or modify
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184 it under the terms of the GNU General Public License as published by
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185 the Free Software Foundation, either version 3 of the License, or
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186 (at your option) any later version.
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187
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188 This program is distributed in the hope that it will be useful,
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189 but WITHOUT ANY WARRANTY; without even the implied warranty of
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190 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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191 GNU General Public License for more details.
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192
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193 You should have received a copy of the GNU General Public License
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194 along with this program. If not, see <http://www.gnu.org/licenses/>.
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195
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196 =cut
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197