* samtools-0.1.5-32 (r449)

[samtools.git] / misc / samtools.pl

diff --git a/misc/samtools.pl b/misc/samtools.pl
index 8c64de85297a20593f9bcadabb021c952c2fdb8e..86b285c5fa6c144a1d60ed61cb48a23bde7f134f 100755 (executable)
--- a/misc/samtools.pl
+++ b/misc/samtools.pl
@@ -302,7 +302,11 @@ sub uniqcmp {
                $p->[0][5]-$p->[1][5], "\n" if ($z && defined($opts{p}) && ($p->[0][3] >= $opts{q} || $p->[1][3] >= $opts{q}));
        } elsif (defined($p->[0])) {
          ++$cnt[$p->[0][3]>=$opts{q}? 6 : 7];
+         print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t*\t0\t*\t",
+               $p->[0][5], "\n" if (defined($opts{p}) && $p->[0][3] >= $opts{q});
        } else {
+         print STDERR "$x\t*\t0\t*\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
+               -$p->[1][5], "\n" if (defined($opts{p}) && $p->[1][3] >= $opts{q});
          ++$cnt[$p->[1][3]>=$opts{q}? 8 : 9];
        }
   }
@@ -326,7 +330,8 @@ sub uniqcmp_aux {
   while (<$fh>) {
        my @t = split;
        next if (@t < 11);
-       my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
+#      my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
+       my $l = 0;
        my ($x, $nm) = (0, 0);
        $nm = $1 if (/NM:i:(\d+)/);
        $_ = $t[5];