From 67b022c34b6a3fc624f813de806e00bd7d625a3e Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 10 Nov 2011 13:27:13 -0500
Subject: [PATCH] Cleanup for new SampleUtils function

-- getVCFHeadersFromRods(rods) is now available so that you don't have getVCFHeadersFromRods(rods, null) throughout the codebase
---
 .../gatk/walkers/varianteval/evaluators/CountVariants.java  | 6 ++++--
 .../gatk/walkers/varianteval/evaluators/G1KPhaseITable.java | 2 +-
 .../sting/gatk/walkers/variantutils/CombineVariants.java    | 2 +-
 .../src/org/broadinstitute/sting/utils/SampleUtils.java     | 2 +-
 .../org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java | 4 ++++
 5 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index e83434037..cba2781d8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -41,6 +41,9 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
     public long nDeletions = 0;
     @DataPoint(description = "Number of complex indels")
     public long nComplex = 0;
+    @DataPoint(description = "Number of symbolic events")
+    public long nSymbolic = 0;
+
     @DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)")
     public long nMixed = 0;
 
@@ -131,8 +134,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     nMixed++;
                     break;
                 case SYMBOLIC:
-                    // ignore symbolic alleles, but don't fail
-                    // todo - consistent way of treating symbolic alleles thgoughout codebase?
+                    nSymbolic++;
                     break;
                 default:
                     throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
index 0e2ee70ef..3ab618496 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java
@@ -103,7 +103,7 @@ public class G1KPhaseITable extends VariantEvaluator {
     }
 
     public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( eval == null ) return null;
+        if ( eval == null || eval.isMonomorphic() ) return null;
 
         switch (eval.getType()) {
 //            case NO_VARIATION:
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index ce03dfffe..573e15971 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -162,7 +162,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
     private boolean sitesOnlyVCF = false;
 
     public void initialize() {
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);
+        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit());
 
         if ( PRIORITY_STRING == null ) {
             PRIORITY_STRING = Utils.join(",", vcfRods.keySet());
diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index edc1413ba..68b220aab 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -150,7 +150,7 @@ public class SampleUtils {
 
         // iterate to get all of the sample names
 
-        for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit, null).entrySet() ) {
+        for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit).entrySet() ) {
             Set<String> vcfSamples = pair.getValue().getGenotypeSamples();
             for ( String sample : vcfSamples )
                 addUniqueSample(samples, sampleOverlapMap, rodNamesToSampleNames, sample, pair.getKey());
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index 3c55c1ff9..5bd6a9b32 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -51,6 +51,10 @@ public class VCFUtils {
         return getVCFHeadersFromRods(toolkit, names);
     }
 
+    public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit) {
+        return getVCFHeadersFromRods(toolkit, (Collection<String>)null);
+    }
+
     public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
         Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();