* samtools-0.1.12-10 (r896)

[samtools.git] / bcftools / vcfutils.pl

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 5df8b0c05e1275e7edc4b8063efa5c585ee7a80a..e38f1ca5ef660eca6aa223d4ab4cfbd359408a2f 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -215,7 +215,7 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #
 }
 
 sub varFilter {
-  my %opts = (d=>2, D=>10000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, G=>0, S=>1000);
+  my %opts = (d=>2, D=>10000000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, G=>0, S=>1000);
   getopts('pd:D:W:Q:w:a:1:2:3:4:G:S:', \%opts);
   die(qq/
 Usage:   vcfutils.pl varFilter [options] <in.vcf>
@@ -289,7 +289,7 @@ Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools.
        $flt = 1 if ($flt == 0 && $mq >= 0 && $mq < $opts{Q});
        $flt = 7 if ($flt == 0 && /PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/
                                 && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4}));
-       $flt = 8 if ($flt == 0 && ((/MXGQ=(\d+)/ && $1 >= $opts{G}) || (/MXSP=(\d+)/ && $1 < $opts{S})));
+       $flt = 8 if ($flt == 0 && ((/MXGQ=(\d+)/ && $1 < $opts{G}) || (/MXSP=(\d+)/ && $1 >= $opts{S})));
 
        my $score = $t[5] * 100 + $dp_alt;
        my $rlen = length($t[3]) - 1; # $indel_score<0 for SNPs
@@ -312,7 +312,10 @@ Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools.
          } else { # SNP or MNP
                for my $x (@staging) {
                  next if (($x->[0]&3) != 3 || $x->[4] + $x->[2] + $ow < $t[1]);
-                 $flt = 5;
+                 if ($x->[4] + length($x->[7]) - 1 == $t[1] && substr($x->[7], -1, 1) eq substr($t[4], 0, 1)
+                         && length($x->[7]) - length($x->[6]) == 1) {
+                       $x->[1] = 5;
+                 } else { $flt = 5; }
                  last;
                }
                # check MNP