Mention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt...

[samtools.git] / misc / wgsim_eval.pl

diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl
index 99e2ac93b1c73fd37525bc963fcc4959a571cf9f..f919a0643a0d2950d8f817c6213a3183f4f9a6dc 100755 (executable)
--- a/misc/wgsim_eval.pl
+++ b/misc/wgsim_eval.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/perl -w
 
 # Contact: lh3
-# Version: 0.1.3
+# Version: 0.1.5
 
 use strict;
 use warnings;
@@ -11,16 +11,18 @@ use Getopt::Std;
 exit;
 
 sub wgsim_eval {
-  my %opts;
-  getopts('pc', \%opts);
-  die("Usage: wgsim_eval.pl [-pc] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
-  my (@c0, @c1);
+  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 = 5;
+  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);
@@ -28,8 +30,11 @@ 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) || $chr eq '*');
        # parse read name and check
@@ -39,19 +44,19 @@ sub wgsim_eval {
          } else {
                if ($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) > $gap);
                  }
                }
          }
@@ -61,14 +66,26 @@ sub wgsim_eval {
        }
        ++$c0[$q];
        ++$c1[$q] unless ($is_correct);
+       @{$fnfp{$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";
+       }
   }
 }