https://github.com/lh3/bwa
Tip revision: 139f68fc4c3747813783a488aef2adc86626b01b authored by Heng Li on 22 September 2022, 23:52:12 UTC
Merge pull request #367 from martin-g/github-actions-linux-aarch64
Merge pull request #367 from martin-g/github-actions-linux-aarch64
Tip revision: 139f68f
qualfa2fq.pl
#!/usr/bin/env perl
use strict;
use warnings;
die("Usage: qualfa2fq.pl <in.fasta> <in.qual>\n") if (@ARGV != 2);
my ($fhs, $fhq, $q);
open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die;
open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die;
$/ = ">"; <$fhs>; <$fhq>; $/ = "\n";
while (<$fhs>) {
$q = <$fhq>;
print "\@$_";
$/ = ">";
$_ = <$fhs>; $q = <$fhq>;
chomp; chomp($q);
$q =~ s/\s*(\d+)\s*/chr($1+33)/eg;
print $_, "+\n";
for (my $i = 0; $i < length($q); $i += 60) {
print substr($q, $i, 60), "\n";
}
$/ = "\n";
}
close($fhs); close($fhq);