X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fwgsim_eval.pl;h=99e2ac93b1c73fd37525bc963fcc4959a571cf9f;hb=0032bb2050f78182baa7fbf9b959540dce4636bd;hp=fe91a3d32403f19c8e5c5a8d330a94fd69f728e6;hpb=7a38b29371a36c4a066a080b178d6ab42494d73a;p=samtools.git

diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl
index fe91a3d..99e2ac9 100755
--- 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);