From 09a5a9eac08ec4b26983bff3c73a0373a91ca688 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 14 Dec 2011 10:43:52 -0500
Subject: [PATCH] Don't update lineNo for decodeLoc - only for decode
 (otherwise they get double-counted).  Even still, because of the way the GATK
 currently utilizes Tribble we can parse the same line multiple times, which
 knocks the line counter out of sync.  For now, I've added a TODO in the code
 to remind us and the error messages note that it's an approximate line
 number.

---
 .../sting/utils/codecs/vcf/AbstractVCFCodec.java              | 3 ++-
 .../broadinstitute/sting/utils/exceptions/UserException.java  | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

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 3009c236b..b902f220f 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
@@ -184,7 +184,6 @@ 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++;
 
         // the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
         if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
@@ -279,6 +278,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
         builder.source(getName());
 
         // increment the line count
+        // TODO -- because of the way the engine utilizes Tribble, we can parse a line multiple times (especially when
+        // TODO --   the first record is far along the contig) and the line counter can get out of sync
         lineNo++;
 
         // parse out the required fields
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index c599d4759..a2816b58f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -184,11 +184,11 @@ public class UserException extends ReviewedStingException {
 
     public static class MalformedVCF extends UserException {
         public MalformedVCF(String message, String line) {
-            super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
+            super(String.format("The provided VCF file is malformed at approximately line %s: %s", line, message));
         }
 
         public MalformedVCF(String message, int lineNo) {
-            super(String.format("The provided VCF file is malformed at line number %d: %s", lineNo, message));
+            super(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message));
         }
     }