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1 #!/usr/bin/perl
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2
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3 use Getopt::Std;
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4 getopts('i:o:O:k:p:', \%opts) ;
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5
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6
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7 # split
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8 $prefix = "primary_$opts{'O'}"."_";
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9 $command = "cd $opts{'p'} && bamtools split -in $opts{'i'} -tag RG -tagPrefix '$prefix' -stub $opts{'p'}/data" ;
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10 #print $command ."\n";
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11 system($command);
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12 chdir($opts{'p'});
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13 # rename to correct format.
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14 my @ls = `ls data.primary_$opts{'O'}_RG_*`;
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15 open OUT, ">$opts{'o'}";
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16 $idx = 0;
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17 foreach(@ls) {
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18 chomp();
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19 my $from = $_;
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20 $from =~ m/(.*_RG_)(.*)(\.bam)/;
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21 my $rg = $2;
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22 # remove data_
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23 my $to = substr($from,5,-4);
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24 $to .= "_visible_bam_$opts{'k'}";
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25 $to =~ s/RG_//;
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26 $to =~ m/primary_(\d+)_(.*)_visible.*/;
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27 $rgreplace = $2;
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28 $rgreplace =~ s/\.|-|_//g;
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29 $to =~ s/(primary_\d+_)(.*)(_visible.*)/$1$rgreplace$3/;
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30 system("mv $from $to");
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31 $idx++;
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32 print OUT "File $idx : $to : ReadGroup: $rg\n";
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33 }
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34 close OUT;
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35 exit;
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36
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37
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