Added comments to umi deduplication
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@ -2,6 +2,7 @@
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use strict;
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use Parallel::ForkManager;
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# this script creats one file with UMI unique reads and one with UMI duplicated reads
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# as input you need aligned sorted by coordinate bam file
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my @torun = ();
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foreach my $file ( <*Aligned.sortedByCoord.out.bam> ) {
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push @torun, $file;
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@ -33,12 +34,12 @@ foreach my $file ( @torun ) {
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my $uniq = join( ':', $chr, $pos, $flag, $tlen, $bc );
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my $pos_ = $pos-1;
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while ( $cigar =~ m/(\d+)([SHMDIN=])/g ) {
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$pos_+=$1 if $2 eq 'M' or $2 eq '=' or $2 eq 'D' or $2 eq 'N';
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$pos_+=$1 if $2 eq 'M' or $2 eq '=' or $2 eq 'D' or $2 eq 'N'; # find position for minus strand
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}
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my $uniq2 = join( ':', $chr, $pos_, $flag, $tlen, $bc );
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if ( exists($duplicates{$id}) or # already marked as duplicate
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( not($flag&16) and ++$seen{ $uniq } > 1 ) or # plus strand
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( $flag&16 and ++$seen{ $uniq2 } > 1 )
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( $flag&16 and ++$seen{ $uniq2 } > 1 ) #minus strand
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) {
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print F2;
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$dups++;
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