my $command = shift(@ARGV);
my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter,
- unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr);
+ unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr, sam2fq=>\&sam2fq);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
}
}
+#
+# sam2fq
+#
+
+sub sam2fq {
+ my %opts = (n=>20, p=>'');
+ getopts('n:p:', \%opts);
+ die("Usage: samtools.pl sam2fq [-n 20] [-p <prefix>] <inp.sam>\n") if (@ARGV == 0 && -t STDIN);
+ if ($opts{p} && $opts{n} > 1) {
+ my $pre = $opts{p};
+ my @fh;
+ for (0 .. $opts{n}-1) {
+ open($fh[$_], sprintf("| gzip > $pre.%.3d.fq.gz", $_)) || die;
+ }
+ my $i = 0;
+ while (<>) {
+ next if (/^@/);
+ chomp;
+ my @t = split("\t");
+ next if ($t[9] eq '*');
+ my ($name, $seq, $qual);
+ if ($t[1] & 16) { # reverse strand
+ $seq = reverse($t[9]);
+ $qual = reverse($t[10]);
+ $seq =~ tr/ACGTacgt/TGCAtgca/;
+ } else {
+ ($seq, $qual) = @t[9,10];
+ }
+ $name = $t[0];
+ $name .= "/1" if ($t[1] & 0x40);
+ $name .= "/2" if ($t[1] & 0x80);
+ print {$fh[$i]} "\@$name\n$seq\n";
+ if ($qual ne '*') {
+ print {$fh[$i]} "+\n$qual\n";
+ }
+ $i = 0 if (++$i == $opts{n});
+ }
+ close($fh[$_]) for (0 .. $opts{n}-1);
+ } else {
+ die("To be implemented.\n");
+ }
+}
+
#
# sra2hdr
#