* samtools.pl-0.2.3

 * change a default parameter

diff --git a/misc/samtools.pl b/misc/samtools.pl
index 4ddc6d11450e30c9138588dcfbeede84a792de92..3dc6fe7d82df9f6255581345790d1477c34f92b7 100755 (executable)
--- a/misc/samtools.pl
+++ b/misc/samtools.pl
@@ -6,7 +6,7 @@ use strict;
 use warnings;
 use Getopt::Std;
 
-my $version = '0.2.2';
+my $version = '0.2.3';
 &usage if (@ARGV < 1);
 
 my $command = shift(@ARGV);
@@ -141,7 +141,7 @@ Options: -d INT        minimum depth to call a SNP [$opts{d}]
 }
 
 sub pileup2fq {
-  my %opts = (d=>3, D=>255, Q=>40, G=>50, l=>10);
+  my %opts = (d=>3, D=>255, Q=>25, G=>50, l=>10);
   getopts('d:D:Q:G:l:', \%opts);
   die(qq/
 Usage:   samtools.pl pileup2fq [options] <in.cns-pileup>
@@ -214,6 +214,9 @@ sub p2q_print_str {
 
 sub usage {
   die(qq/
+Program: samtools.pl (helper script for SAMtools)
+Version: $version
+Contact: Heng Li <lh3\@sanger.ac.uk>\n
 Usage:   samtools.pl <command> [<arguments>]\n
 Command: indelFilter   filter indels generated by `pileup -c'
          snpFilter     filter SNPs generated by `pileup -c'