From 0f7c917e7a04d878a7c3a9aacd571a75f218c908 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 17 May 2012 13:36:42 -0400
Subject: [PATCH] Better error checking and messages for bad alleles

---
 .../sting/utils/codecs/vcf/AbstractVCFCodec.java             | 5 ++++-
 .../broadinstitute/sting/utils/variantcontext/Allele.java    | 2 +-
 2 files changed, 5 insertions(+), 2 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 2fcc3ec2f..949f488c8 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
@@ -693,7 +693,10 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
                 if ( a.isSymbolic() ) {
                     clippedAlleles.add(a);
                 } else {
-                    clippedAlleles.add(Allele.create(Arrays.copyOfRange(a.getBases(), forwardClipping, a.getBases().length-reverseClipping), a.isReference()));
+                    final byte[] allele = Arrays.copyOfRange(a.getBases(), forwardClipping, a.getBases().length-reverseClipping);
+                    if ( !Allele.acceptableAlleleBases(allele) )
+                        generateException("Unparsable vcf record with bad allele [" + allele + "]", lineNo);
+                    clippedAlleles.add(Allele.create(allele, a.isReference()));
                 }
             }
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
index 2ca3e0055..0affcc070 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
@@ -160,7 +160,7 @@ public class Allele implements Comparable<Allele> {
                 case 'G': case 'g' : return isRef ? REF_G : ALT_G;
                 case 'T': case 't' : return isRef ? REF_T : ALT_T;
                 case 'N': case 'n' : return isRef ? REF_N : ALT_N;
-                default: throw new IllegalArgumentException("Illegal base: " + (char)bases[0]);
+                default: throw new IllegalArgumentException("Illegal base [" + (char)bases[0] + "] seen in the allele");
             }
         } else {
             return new Allele(bases, isRef);