* samtools-0.1.5-31 (r448)

[samtools.git] / misc / wgsim_eval.pl

diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl
index 412243f9a5485a1962473fe4ce4dd3559a4e3597..01038f1fab67c6585e2788eb19e2ae4a6e015ab2 100755 (executable)
--- a/misc/wgsim_eval.pl
+++ b/misc/wgsim_eval.pl
@@ -30,8 +30,11 @@ sub wgsim_eval {
        $_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
        --$rght;
        # correct for soft clipping
+       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) || $chr eq '*');
        # parse read name and check
@@ -41,19 +44,19 @@ sub wgsim_eval {
          } else {
                if ($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
-                       $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
-                       $is_correct = 0 if (abs($3 - $left) > $gap);
+                       $is_correct = 0 if (abs($3 - $left) > $gap && abs($3 - $left0) > $gap);
                  } 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
-                       $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 {
-                       $is_correct = 0 if (abs($2 - $left) > $gap);
+                       $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
                  }
                }
          }