From 718da7757e75a2367da8b1e6351ceef60bf76c47 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 7 Feb 2012 13:15:58 -0500
Subject: [PATCH] Fixes to ValidateVariants as per GS post: ref base of mixed
 alleles were sometimes wrong, error print out of bad ACs was throwing a
 RuntimeException, don't validate ACs if there are no genotypes.

---
 .../gatk/walkers/variantutils/ValidateVariants.java   | 11 +++++------
 .../sting/utils/variantcontext/VariantContext.java    |  8 +++++++-
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index fdfca982c..530258fe0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -128,13 +128,13 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
 
         // get the true reference allele
         Allele reportedRefAllele = vc.getReference();
-        Allele observedRefAllele;
+        Allele observedRefAllele = null;
         // insertions
         if ( vc.isSimpleInsertion() ) {
             observedRefAllele = Allele.create(Allele.NULL_ALLELE_STRING);
         }
         // deletions
-        else if ( vc.isSimpleDeletion() || vc.isMixed() || vc.isMNP() ) {
+        else if ( vc.isSimpleDeletion() || vc.isMNP() ) {
             // we can't validate arbitrarily long deletions
             if ( reportedRefAllele.length() > 100 ) {
                 logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", reportedRefAllele.length(), vc.getChr(), vc.getStart()));
@@ -143,16 +143,15 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
 
             // deletions are associated with the (position of) the last (preceding) non-deleted base;
             // hence to get actually deleted bases we need offset = 1
-            int offset = 1 ;
-            if ( vc.isMNP() ) offset = 0; // if it's an MNP, the reported position IS the first modified base
+            int offset = vc.isMNP() ? 0 : 1;
             byte[] refBytes = ref.getBases();
             byte[] trueRef = new byte[reportedRefAllele.length()];
             for (int i = 0; i < reportedRefAllele.length(); i++)
                 trueRef[i] = refBytes[i+offset];
             observedRefAllele = Allele.create(trueRef, true);
         }
-        // SNPs, etc.
-        else {
+        // SNPs, etc. but not mixed types because they are too difficult
+        else if ( !vc.isMixed() ) {
             byte[] refByte = new byte[1];
             refByte[0] = ref.getBase();
             observedRefAllele = Allele.create(refByte, true);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 247e412dd..27721be95 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -920,6 +920,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     }
 
     public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
+        if ( reference == null )
+            return;
+
         // don't validate if we're a complex event
         if ( !isComplexIndel() && !reference.isNull() && !reference.basesMatch(getReference()) ) {
             throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
@@ -963,6 +966,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     }
 
     public void validateChromosomeCounts() {
+        if ( !hasGenotypes() )
+            return;
+        
         // AN
         if ( hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) {
             int reportedAN = Integer.valueOf(getAttribute(VCFConstants.ALLELE_NUMBER_KEY).toString());
@@ -993,7 +999,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
                     throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag doesn't have the correct number of values for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedACs.size(), observedACs.size()));
                 for (int i = 0; i < observedACs.size(); i++) {
                     if ( Integer.valueOf(reportedACs.get(i).toString()) != observedACs.get(i) )
-                        throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedACs.get(i), observedACs.get(i)));
+                        throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %s vs. %d", getChr(), getStart(), reportedACs.get(i), observedACs.get(i)));
                 }
             } else {
                 if ( observedACs.size() != 1 )