--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/next_gen_conversion/bwa_solid2fastq_modified.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,89 @@
+#!/usr/bin/perl -w
+
+# Author: lh3
+# Note: Ideally, this script should be written in C. It is a bit slow at present.
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+my %opts;
+my $version = '0.1.3';
+my $usage = qq{
+Usage: solid2fastq.pl <paired> <outfile1> <outfile2> <F3.csfasta> <F3.qual> <R3.csfasta> <R3.qual> 
+
+Note: <in.title> is the string showed in the `# Title:' line of a
+      ".csfasta" read file. Then <in.title>F3.csfasta is read sequence
+      file and <in.title>F3_QV.qual is the quality file. If
+      <in.title>R3.csfasta is present, this script assumes reads are
+      paired; otherwise reads will be regarded as single-end.
+
+      The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3
+      tag and `2' for F3. Usually you may want to use short <out.prefix>
+      to save diskspace. Long <out.prefix> also causes troubles to maq.
+
+};
+
+getopts('', \%opts);
+die($usage) if (@ARGV != 7);
+my ($is_paired,$outfile1,$outfile2,$f3reads,$f3qual,$r3reads,$r3qual) = @ARGV;
+my (@fhr, @fhw);
+my $fn = '';
+my @fn_suff = ($f3reads,$f3qual,$r3reads,$r3qual);
+if ($is_paired eq "yes") { # paired end
+  for (0 .. 3) {
+	$fn = $fn_suff[$_];
+	$fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
+	open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
+  }
+  open($fhw[0], "|gzip >$outfile2") || die;
+  open($fhw[1], "|gzip >$outfile1") || die;
+  my (@df, @dr);
+  @df = &read1(1); @dr = &read1(2);
+  while (@df && @dr) {
+	if ($df[0] eq $dr[0]) { # mate pair
+	  print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1];
+	  @df = &read1(1); @dr = &read1(2);
+	}
+  }
+  close($fhr[$_]) for (0 .. $#fhr);
+  close($fhw[$_]) for (0 .. $#fhw);
+} else { # single end
+  for (0 .. 1) {
+	my $fn = "$fn_suff[$_]";
+	$fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
+	open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
+  }
+  open($fhw[2], "|gzip >$outfile1") || die;
+  my @df;
+  while (@df = &read1(1, $fhr[0], $fhr[1])) {
+	print {$fhw[2]} $df[1];
+  }
+  close($fhr[$_]) for (0 .. $#fhr);
+  close($fhw[2]);
+}
+
+sub read1 {
+  my $i = shift(@_);
+  my $j = ($i-1)<<1;
+  my ($key, $seq);
+  my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]);
+  while (<$fhs>) {
+	my $t = <$fhq>;
+	if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) {
+	  $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines
+	  #print $key;
+	  die(qq/** unmatched read name: '$_' != '$t'\n/) unless ($_ eq $t);
+	  my $name = "$1_$2_$3/$i";
+	  $_ = substr(<$fhs>, 2);
+	  tr/0123./ACGTN/;
+	  my $s = $_;
+	  $_ = <$fhq>;
+	  s/^(\d+)\s*//;
+	  s/(\d+)\s*/chr($1+33)/eg;
+	  $seq = qq/\@$name\n$s+\n$_\n/;
+	  last;
+	} 
+  }
+  return defined($seq)? ($key, $seq) : ();
+}