From 4bde24f0201512ca39828f3a681c6dbd3a1d5584 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 21 May 2012 16:24:23 -0400
Subject: [PATCH] Bugfix for VCFWriter in the case where there are no genotypes
 in the VC but genotypes in the header

---
 .../utils/variantcontext/writer/BCF2Writer.java     |  4 ++--
 .../utils/variantcontext/writer/VCFWriter.java      | 13 +++++--------
 2 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
index 446d37dec..1bfcfc0b5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
@@ -162,7 +162,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
         // info fields
         final int nAlleles = vc.getNAlleles();
         final int nInfo = vc.getAttributes().size();
-        final int nGenotypeFormatFields = VCFWriter.calcVCFGenotypeKeys(vc).size();
+        final int nGenotypeFormatFields = VCFWriter.calcVCFGenotypeKeys(vc, header).size();
         final int nSamples = vc.getNSamples();
 
         encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x00FF), BCF2Type.INT32);
@@ -207,7 +207,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
     }
 
     private byte[] buildSamplesData(final VariantContext vc) throws IOException {
-        List<String> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc);
+        List<String> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc, header);
         for ( final String field : genotypeFields ) {
             if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
                 addGenotypes(vc);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
index 10eeb2778..d22c68feb 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
@@ -254,13 +254,10 @@ class VCFWriter extends IndexingVariantContextWriter {
                 mWriter.write(VCFConstants.FIELD_SEPARATOR);
                 mWriter.write(((LazyGenotypesContext)gc).getUnparsedGenotypeData().toString());
             } else {
-                List<String> genotypeAttributeKeys = new ArrayList<String>();
-                if ( vc.hasGenotypes() ) {
-                    genotypeAttributeKeys.addAll(calcVCFGenotypeKeys(vc));
-                }
+                List<String> genotypeAttributeKeys = calcVCFGenotypeKeys(vc, mHeader);
+                if ( ! genotypeAttributeKeys.isEmpty() ) {
+                    final String genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
 
-                if ( genotypeAttributeKeys.size() > 0 ) {
-                    String genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
                     mWriter.write(VCFConstants.FIELD_SEPARATOR);
                     mWriter.write(genotypeFormatString);
 
@@ -472,7 +469,7 @@ class VCFWriter extends IndexingVariantContextWriter {
      * @param vc
      * @return an ordered list of genotype fields in use in VC.  If vc has genotypes this will always include GT first
      */
-    public static List<String> calcVCFGenotypeKeys(VariantContext vc) {
+    public static List<String> calcVCFGenotypeKeys(final VariantContext vc, final VCFHeader header) {
         Set<String> keys = new HashSet<String>();
 
         boolean sawGoodGT = false;
@@ -504,7 +501,7 @@ class VCFWriter extends IndexingVariantContextWriter {
             sortedList = newList;
         }
 
-        if ( sortedList.isEmpty() && vc.hasGenotypes() ) {
+        if ( sortedList.isEmpty() && header.hasGenotypingData() ) {
             // this needs to be done in case all samples are no-calls
             return Collections.singletonList(VCFConstants.GENOTYPE_KEY);
         } else {