Fixing/cleaning up the vcf merge util

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3047 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java

@@ -90,20 +90,6 @@ public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Ite
         return mCurrentRecord.getNonRefAlleleFrequency();
     }
 
-    public boolean hasStrandBias() {
-        assertNotNull();
-        return this.mCurrentRecord.getInfoValues().containsKey(VCFRecord.STRAND_BIAS_KEY);
-    }
-
-    /**
-     * get the strand bias of this variant
-     *
-     * @return StrandBias with the stored slod
-     */
-    public double getStrandBias() {
-        return hasStrandBias() ? Double.valueOf(this.mCurrentRecord.getInfoValues().get(VCFRecord.STRAND_BIAS_KEY)) : 0.0;
-    }
-
     /** @return the VARIANT_TYPE of the current variant */
     public Variation.VARIANT_TYPE getType() {
         assertNotNull();

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java

@@ -69,14 +69,10 @@ public class VCFUtils {
         VCFParameters params = new VCFParameters();
         params.addFormatItem(VCFGenotypeRecord.GENOTYPE_KEY);
 
-        // keep track of the locus specific data so we can merge them intelligently
+        // keep track of the data so we can merge them intelligently
-        int totalReadDepth = 0;
         double maxConfidence = 0.0;
-        double totalSLOD = 0.0;
-        int SLODsSeen = 0;
-        double totalFreq = 0.0;
-        int freqsSeen = 0;
         String id = null;
+        Map<String, String> infoFields = new HashMap<String, String>();
         List<String> filters = new ArrayList<String>();
 
         for ( RodVCF rod : rods ) {
@@ -87,9 +83,6 @@ public class VCFUtils {
                 if ( params.getPosition() < 1 )
                     params.setLocations(rod.getLocation(), call.getReference());
                 params.addGenotypeRecord(createVCFGenotypeRecord(params, call, rod.mCurrentRecord));
-                int depth = call.getReadCount();
-                if ( depth > 0 )
-                    totalReadDepth += call.getReadCount();
             }
 
             // set the overall confidence to be the max entry we see
@@ -97,32 +90,16 @@ public class VCFUtils {
             if ( confidence > maxConfidence )
                 maxConfidence = confidence;
 
-            if ( !rod.isReference() && rod.hasNonRefAlleleFrequency() ) {
-                totalFreq += rod.getNonRefAlleleFrequency();
-                freqsSeen++;
-            }
-
-            if ( rod.hasStrandBias() ) {
-                totalSLOD += rod.getStrandBias();
-                SLODsSeen++;
-            }
-
             if ( rod.getID() != null )
                 id = rod.getID();
 
             if ( rod.isFiltered() )
                 filters.add(rod.getFilterString());
+
+            // just take the last value we see for a given key
+            infoFields.putAll(rod.getInfoValues());
         }
 
-        Map<String, String> infoFields = new HashMap<String, String>();
-        infoFields.put(VCFRecord.DEPTH_KEY, String.format("%d", totalReadDepth));
-
-        // set the overall strand bias and allele frequency to be the average of all entries we've seen
-        if ( SLODsSeen > 0 )
-            infoFields.put(VCFRecord.STRAND_BIAS_KEY, String.format("%.2f", (totalSLOD/(double)SLODsSeen)));
-        if ( freqsSeen > 0 )
-            infoFields.put(VCFRecord.ALLELE_FREQUENCY_KEY, String.format("%.2f", (totalFreq/(double)freqsSeen)));
-                
         return new VCFRecord(params.getReferenceBases(),
                 params.getContig(),
                 params.getPosition(),
@@ -152,16 +129,10 @@ public class VCFUtils {
         }
 
         VCFGenotypeRecord record = new VCFGenotypeRecord(gtype.getSampleName(), alleles, VCFGenotypeRecord.PHASE.UNPHASED);
-
+        for ( Map.Entry<String, String> entry : gtype.getFields().entrySet() ) {
-        // calculate the genotype quality and the read depth
+            record.setField(entry.getKey(), entry.getValue());
-        record.setField(VCFGenotypeRecord.DEPTH_KEY, String.valueOf(gtype.getReadCount()));
+            params.addFormatItem(entry.getKey());
-        params.addFormatItem(VCFGenotypeRecord.DEPTH_KEY);
+        }
-        double qual = Math.min(10.0 * gtype.getNegLog10PError(), VCFGenotypeRecord.MAX_QUAL_VALUE);
-        if ( qual >= 0 )
-            record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual));
-        else
-            record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%d", VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY));
-        params.addFormatItem(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
 
         record.setVCFRecord(vcfrecord);
         return record;

java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java

@@ -10,35 +10,35 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
         return "-T CallsetConcordance -R " + oneKGLocation + "reference/human_b36_both.fasta -L 1:1-8000 -CO %s";
     }
 
-    //@Test
+    @Test
     public void testSimpleVenn() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn", 1,
-                Arrays.asList("cdd027a0d7bbfae2ba75480fcaa14356"));
+                Arrays.asList("d9124d2b0fb5bec5bc50c26a16b4e900"));
         executeTest("testSimpleVenn", spec);
     }
 
-    //@Test
+    @Test
     public void testSNPConcordance() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1,
-                Arrays.asList("310bf0824fc407b2e40cbbaea234471e"));
+                Arrays.asList("df1fbc744947f316f65f51a21368b0e4"));
         executeTest("testSNPConcordance", spec);
     }
 
-    //@Test
+    @Test
     public void testNWayVenn() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -B set3,VCF," + validationDataLocation + "CEU.sample.vcf -CT NWayVenn", 1,
-                Arrays.asList("179adafae6efdc879fc22442ab9e599f"));
+                Arrays.asList("aa835ae5368b35f376b844d7f8ef2976"));
         executeTest("testNWayVenn", spec);
     }
 
-    //@Test
+    @Test
     public void testMulti() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn -CT NWayVenn -CT SNPGenotypeConcordance:qscore=5", 1,
-                Arrays.asList("c8fe63633ef6ed2b6068958f06cddfe0"));
+                Arrays.asList("c9ef68cc3b7dc08f1d2b49170e6560ab"));
         executeTest("testMulti", spec);
     }