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executable file 26 lines (23 sloc) 730 Bytes
#!/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!
my $seq = $t[9];
my $phred = $t[10];
# if alternative alignment has other orientation than primary,
# then print the reverse (complement) of sequence and phred string
if ((($t[1]&0x10)>0) xor ($2<0)) {
$seq = reverse $seq;
$seq =~ tr/ACGTacgt/TGCAtgca/;
$phred = reverse $phred;
}
print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, $seq, $phred, "NM:i:$4"), "\n");
}
} else { print; }
}