X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fwgsim_eval.pl;h=f919a0643a0d2950d8f817c6213a3183f4f9a6dc;hb=9f118264ea012adc21a46d7c03eaad4f9ce7d4d4;hp=fe91a3d32403f19c8e5c5a8d330a94fd69f728e6;hpb=7a38b29371a36c4a066a080b178d6ab42494d73a;p=samtools.git

diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl
index fe91a3d..f919a06 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: 0.1.5
 
 use strict;
 use warnings;
@@ -11,13 +11,18 @@ use Getopt::Std;
 exit;
 
 sub wgsim_eval {
-  my %opts;
-  getopts('p', \%opts);
-  die("Usage: wgsim_eval.pl [-p] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
-  my (@c0, @c1);
-  my $max_q = 0;
+  my %opts = (g=>5);
+  getopts('pcag:', \%opts);
+  die("Usage: wgsim_eval.pl [-pca] [-g $opts{g}] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
+  my (@c0, @c1, %fnfp);
+  my ($max_q, $flag) = (0, 0);
+  my $gap = $opts{g};
+  $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);
@@ -25,36 +30,62 @@ sub wgsim_eval {
 	$_ = $t[5]; s/(\d+)[MDN]/$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) || $chr eq '*');
 	# parse read name and check
-	++$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 && abs($2 - $left0) > $gap);
+		  } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
+			$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 && abs($3 - $left0) > $gap);
+		  } else { # R3, reverse
+			$is_correct = 0 if (abs($2 - $rght) > $gap && abs($3 - $rght0) > $gap);
+		  }
 		} else {
-		  $is_correct = 0 if (abs($2 - $left) > 5);
+		  if ($t[1] & 0x10) { # reverse
+			$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 && abs($2 - $left0) > $gap);
+		  }
 		}
-	  } else {
-		die("[wgsim_eval] bug in wgsim?\n");
 	  }
 	} else {
-	  die("[wgsim_eval] read '$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 && $q > 0);
+	@{$fnfp{$t[4]}} = (0, 0) unless (defined $fnfp{$t[4]});
+	++$fnfp{$t[4]}[0];
+	++$fnfp{$t[4]}[1] unless ($is_correct);
+	print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
   }
   # print
   my ($cc0, $cc1) = (0, 0);
-  for (my $i = $max_q; $i >= 0; --$i) {
-	$c0[$i] = 0 unless (defined $c0[$i]);
-	$c1[$i] = 0 unless (defined $c1[$i]);
-	$cc0 += $c0[$i]; $cc1 += $c1[$i];
-	printf("%.2dx %12d / %-12d  %12d  %.3e\n", $i, $c1[$i], $c0[$i], $cc0, $cc1/$cc0);
+  if (!defined($opts{a})) {
+	for (my $i = $max_q; $i >= 0; --$i) {
+	  $c0[$i] = 0 unless (defined $c0[$i]);
+	  $c1[$i] = 0 unless (defined $c1[$i]);
+	  $cc0 += $c0[$i]; $cc1 += $c1[$i];
+	  printf("%.2dx %12d / %-12d  %12d  %.3e\n", $i, $c1[$i], $c0[$i], $cc0, $cc1/$cc0) if ($cc0);
+	}
+  } else {
+	for (reverse(sort {$a<=>$b} (keys %fnfp))) {
+	  next if ($_ == 0);
+	  $cc0 += $fnfp{$_}[0];
+	  $cc1 += $fnfp{$_}[1];
+	  print join("\t", $_, $cc0, $cc1), "\n";
+	}
   }
 }