diff --git a/xa2multi.pl b/xa2multi.pl new file mode 100755 index 0000000..6dae38b --- /dev/null +++ b/xa2multi.pl @@ -0,0 +1,16 @@ +#!/usr/bin/perl -w + +use strict; +use warnings; + +while (<>) { + if (/\tXA:Z:(\S+)/) { + my $l = $1; + print; + my @t = split("\t"); + while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) { + my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated! + print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, @t[9..10], "NM:i:$4"), "\n"); + } + } else { print; } +}