parse_bam_flag.pl

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <bam_flag>\n";
my $flag = shift or die $usage;

die "Please enter a numerical value\n" if $flag =~ /\D+/;

if ($flag & 0x1){
   print "template having multiple segments in sequencing\n";
}
if ($flag & 0x2){
   print "each segment properly aligned according to the aligner\n";
}
if ($flag & 0x4){
   print "segment unmapped\n";
}
if ($flag & 0x8){
   print "next segment in the template unmapped\n";
}
if ($flag & 0x10){
   print "SEQ being reverse complemented\n";
}
if ($flag & 0x20){
   print "SEQ of the next segment in the template being reversed\n";
}
if ($flag & 0x40){
   print "the first segment in the template\n";
}
if ($flag & 0x80){
   print "the last segment in the template\n";
}
if ($flag & 0x100){
   print "secondary alignment\n";
}
if ($flag & 0x200){
   print "not passing quality controls\n";
}
if ($flag & 0x400){
   print "PCR or optical duplicate\n";
}
if ($flag & 0x800){
   print "supplementary alignment\n";
}

exit(0);

__END__