diff bwa-0.6.2/qualfa2fq.pl @ 2:a294fbfcb1db draft default tip

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/qualfa2fq.pl	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,27 @@
+#!/usr/bin/perl -w
+
+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);