17 lines
415 B
Perl
17 lines
415 B
Perl
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#!/usr/bin/perl -w
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use strict;
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use warnings;
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while (<>) {
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if (/\tXA:Z:(\S+)/) {
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my $l = $1;
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print;
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my @t = split("\t");
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while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) {
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my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated!
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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");
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}
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} else { print; }
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}
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