From: Heng Li <lh3@live.co.uk>
Date: Tue, 7 Dec 2010 19:43:54 +0000 (+0000)
Subject: fixed a bug in vcf2fq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=8a29cb371f7c4c858b75e00efb1d78950c765c7a;p=samtools.git

fixed a bug in vcf2fq
---

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 3e5b7b2..63509e8 100755
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -484,11 +484,12 @@ Options: -d INT    minimum depth          [$opts{d}]
 	  $seq = $qual = '';
 	  @gaps = ();
 	}
-	if ($t[1] - $last_pos != 1) {
+	die("[vcf2fq] unsorted input\n") if ($t[1] - $last_pos < 0);
+	if ($t[1] - $last_pos > 1) {
 	  $seq .= 'n' x ($t[1] - $last_pos - 1);
 	  $qual .= '!' x ($t[1] - $last_pos - 1);
 	}
-	if (length($t[3]) == 1 && $t[4] =~ /^([A-Za-z.])(,[A-Za-z])*$/) { # a SNP or reference
+	if (length($t[3]) == 1 && $t[7] !~ /INDEL/ && $t[4] =~ /^([A-Za-z.])(,[A-Za-z])*$/) { # a SNP or reference
 	  my ($ref, $alt) = ($t[3], $1);
 	  my ($b, $q);
 	  $q = $1 if ($t[7] =~ /FQ=(-?[\d\.]+)/);
@@ -546,7 +547,7 @@ Command: subsam       get a subset of samples
          ucscsnp2vcf  convert UCSC SNP SQL dump to VCF
 
          varFilter    filtering short variants (*)
-         vcf2fq       VCF->fastq (*)
+         vcf2fq       VCF->fastq (**)
 
 Notes: Commands with description endting with (*) may need bcftools
        specific annotations.