* samtools.pl-0.2.0

[samtools.git] / misc / wgsim_eval.pl

diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl
index fe91a3d32403f19c8e5c5a8d330a94fd69f728e6..99e2ac93b1c73fd37525bc963fcc4959a571cf9f 100755 (executable)
--- a/misc/wgsim_eval.pl
+++ b/misc/wgsim_eval.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/perl -w
 
 # Contact: lh3
-# Version: 0.1.2
+# Version: 0.1.3
 
 use strict;
 use warnings;
@@ -12,10 +12,13 @@ exit;
 
 sub wgsim_eval {
   my %opts;
-  getopts('p', \%opts);
-  die("Usage: wgsim_eval.pl [-p] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
+  getopts('pc', \%opts);
+  die("Usage: wgsim_eval.pl [-pc] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
   my (@c0, @c1);
-  my $max_q = 0;
+  my ($max_q, $flag) = (0, 0);
+  my $gap = 5;
+  $flag |= 1 if (defined $opts{p});
+  $flag |= 2 if (defined $opts{c});
   while (<>) {
        my @t = split;
        my $line = $_;
@@ -30,24 +33,35 @@ sub wgsim_eval {
        # skip unmapped reads
        next if (($t[1]&0x4) || $chr eq '*');
        # parse read name and check
-       ++$c0[$q];
        if ($t[0] =~ /^(\S+)_(\d+)_(\d+)_/) {
          if ($1 ne $chr) { # different chr
                $is_correct = 0;
-         } elsif ($2 < $3) { # should always be true if reads are generated from wgsim
-               if ($t[1] & 0x10) { # reverse
-                 $is_correct = 0 if (abs($3 - $rght) > 5); # in case of indels that are close to the end of a reads
+         } else {
+               if ($flag & 2) {
+                 if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward
+                       $is_correct = 0 if (abs($2 - $left) > $gap);
+                 } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
+                       $is_correct = 0 if (abs($3 - $rght) > $gap);
+                 } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward
+                       $is_correct = 0 if (abs($3 - $left) > $gap);
+                 } else { # R3, reverse
+                       $is_correct = 0 if (abs($2 - $rght) > $gap);
+                 }
                } else {
-                 $is_correct = 0 if (abs($2 - $left) > 5);
+                 if ($t[1] & 0x10) { # reverse
+                       $is_correct = 0 if (abs($3 - $rght) > $gap); # in case of indels that are close to the end of a reads
+                 } else {
+                       $is_correct = 0 if (abs($2 - $left) > $gap);
+                 }
                }
-         } else {
-               die("[wgsim_eval] bug in wgsim?\n");
          }
        } else {
-         die("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
+         warn("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
+         next;
        }
+       ++$c0[$q];
        ++$c1[$q] unless ($is_correct);
-       print STDERR $line if (defined($opts{p}) && !$is_correct && $q > 0);
+       print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
   }
   # print
   my ($cc0, $cc1) = (0, 0);