From a340a1aeaca727d91c0d0cae943a12bec69c84f6 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 4 Nov 2011 11:44:24 -0400
Subject: [PATCH] Bug fix.  decodeLoc() should update lineNo so you get
 meaningful line no when indexing

due to malformed VCF files.
---
 .../broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index 07a61ae36..3212e3904 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -162,6 +162,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
      * @return a feature, (not guaranteed complete) that has the correct start and stop
      */
     public Feature decodeLoc(String line) {
+        lineNo++;
         String[] locParts = new String[6];
         int nParts = ParsingUtils.split(line, locParts, VCFConstants.FIELD_SEPARATOR_CHAR, true);