Imported Upstream version 0.1.6~dfsg

[samtools.git] / misc / wgsim_eval.pl

diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl
index 99e2ac93b1c73fd37525bc963fcc4959a571cf9f..01038f1fab67c6585e2788eb19e2ae4a6e015ab2 100755 (executable)
--- a/misc/wgsim_eval.pl
+++ b/misc/wgsim_eval.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/perl -w
 
 # Contact: lh3
 #!/usr/bin/perl -w
 
 # Contact: lh3

-# Version: 0.1.3
+# Version: 0.1.5

 
 use strict;
 use warnings;
 
 use strict;
 use warnings;


@@ -11,16 +11,18 @@ use Getopt::Std;
 exit;
 
 sub wgsim_eval {
 exit;
 
 sub wgsim_eval {

-  my %opts;
-  getopts('pc', \%opts);
-  die("Usage: wgsim_eval.pl [-pc] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
+  my %opts = (g=>5);
+  getopts('pcg:', \%opts);
+  die("Usage: wgsim_eval.pl [-pc] [-g $opts{g}] <in.sam>\n") if (@ARGV == 0 && -t STDIN);

   my (@c0, @c1);
   my ($max_q, $flag) = (0, 0);
   my (@c0, @c1);
   my ($max_q, $flag) = (0, 0);

-  my $gap = 5;
+  my $gap = $opts{g};

   $flag |= 1 if (defined $opts{p});
   $flag |= 2 if (defined $opts{c});
   while (<>) {
   $flag |= 1 if (defined $opts{p});
   $flag |= 2 if (defined $opts{c});
   while (<>) {

-       my @t = split;
+       next if (/^\@/);
+       my @t = split("\t");
+       next if (@t < 11);

        my $line = $_;
        my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1, $t[2], $t[3], $t[3]);
        $max_q = $q if ($q > $max_q);
        my $line = $_;
        my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1, $t[2], $t[3], $t[3]);
        $max_q = $q if ($q > $max_q);


@@ -28,8 +30,11 @@ sub wgsim_eval {
        $_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
        --$rght;
        # correct for soft clipping
        $_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
        --$rght;
        # correct for soft clipping

-       $left -= $1 if (/^(\d+)S/);
-       $rght += $1 if (/(\d+)S$/);
+       my ($left0, $rght0) = ($left, $rght);
+       $left -= $1 if (/^(\d+)[SH]/);
+       $rght += $1 if (/(\d+)[SH]$/);
+       $left0 -= $1 if (/(\d+)[SH]$/);
+       $rght0 += $1 if (/^(\d+)[SH]/);

        # skip unmapped reads
        next if (($t[1]&0x4) || $chr eq '*');
        # parse read name and check
        # skip unmapped reads
        next if (($t[1]&0x4) || $chr eq '*');
        # parse read name and check


@@ -39,19 +44,19 @@ sub wgsim_eval {
          } else {
                if ($flag & 2) {
                  if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward
          } else {
                if ($flag & 2) {
                  if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward

-                       $is_correct = 0 if (abs($2 - $left) > $gap);
+                       $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);

                  } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
                  } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse

-                       $is_correct = 0 if (abs($3 - $rght) > $gap);
+                       $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap);

                  } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward
                  } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward

-                       $is_correct = 0 if (abs($3 - $left) > $gap);
+                       $is_correct = 0 if (abs($3 - $left) > $gap && abs($3 - $left0) > $gap);

                  } else { # R3, reverse
                  } else { # R3, reverse

-                       $is_correct = 0 if (abs($2 - $rght) > $gap);
+                       $is_correct = 0 if (abs($2 - $rght) > $gap && abs($3 - $rght0) > $gap);

                  }
                } else {
                  if ($t[1] & 0x10) { # reverse
                  }
                } else {
                  if ($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
+                       $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap); # in case of indels that are close to the end of a reads

                  } else {
                  } else {

-                       $is_correct = 0 if (abs($2 - $left) > $gap);
+                       $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);

                  }
                }
          }
                  }
                }
          }