-Added convenience method to VCF record to tell if it's a no call and have rodVCF use it before querying for info fields

-Don't restrict info fields to 2-letter keys
[about to move these to core]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2002 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -304,13 +304,17 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
             if (lst.size() != 1) {
                 throw new IllegalStateException("VCF object does not have one and only one genotype record");
             }
+            VCFGenotypeRecord rec = lst.get(0);
+            if ( rec.isEmptyGenotype() )
+                return null;
+
             double qual = 0;
-            if (lst.get(0).getAlleles().equals(this.getReference()))
+            if (rec.getAlleles().equals(this.getReference()))
                 qual = refQual;
-            else if (lst.get(0).getFields().containsKey("GQ"))
-                qual = Double.valueOf(lst.get(0).getFields().get("GQ")) / 10.0;
-            int coverage = (lst.get(0).getFields().containsKey("RD") ? Integer.valueOf(lst.get(0).getFields().get("RD")) : 0);
-            return new VCFGenotypeCall(this.getReference().charAt(0), this.getLocation(), Utils.join("", lst.get(0).getAlleles()), qual, coverage, lst.get(0).getSampleName());
+            else if (rec.getFields().containsKey("GQ"))
+                qual = Double.valueOf(rec.getFields().get("GQ")) / 10.0;
+            int coverage = (rec.getFields().containsKey("RD") ? Integer.valueOf(rec.getFields().get("RD")) : 0);
+            return new VCFGenotypeCall(this.getReference().charAt(0), this.getLocation(), Utils.join("", rec.getAlleles()), qual, coverage, rec.getSampleName());
         }
         return null;
     }
@@ -329,6 +333,9 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         double refQual = (this.getNegLog10PError());
         // add the reference
         for (VCFGenotypeRecord rec : mCurrentRecord.getVCFGenotypeRecords()) {
+            if ( rec.isEmptyGenotype() )
+                continue;
+ ;
             double qual = 0;
             if (rec.getAlleles().equals(this.getReference()))
                 qual = refQual;

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/IndelSubsets.java

@@ -101,5 +101,5 @@ public class IndelSubsets implements ConcordanceType {
         return Math.max(leftRun, rightRun);
     }
 
-    public String getInfoName() { return "IS"; }    
+    public String getInfoName() { return "IndelSubsets"; }    
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/NWayVenn.java

@@ -32,11 +32,11 @@ public class NWayVenn implements ConcordanceType {
         while ( iter.hasNext() ) {
             tag.append(iter.next());
             if ( iter.hasNext() )
-                tag.append(".");
+                tag.append("-");
         }
 
         return tag.toString();
     }
 
-    public String getInfoName() { return "NV"; }    
+    public String getInfoName() { return "NwayVenn"; }    
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java

@@ -94,5 +94,5 @@ public class SNPGenotypeConcordance implements ConcordanceType {
         return altAllele1 == altAllele2;
     }
 
-    public String getInfoName() { return "SG"; }    
+    public String getInfoName() { return "SnpConcordance"; }    
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java

@@ -58,5 +58,5 @@ public class SimpleVenn implements ConcordanceType {
         return "concordant";
     }
 
-    public String getInfoName() { return "SV"; }
+    public String getInfoName() { return "Venn"; }
 }

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

@@ -115,6 +115,13 @@ public class VCFGenotypeRecord {
 
     }
 
+    public boolean isEmptyGenotype() {
+        for ( VCFGenotypeEncoding encoding : mGenotypeAlleles ) {
+            if ( encoding.getType() != VCFGenotypeEncoding.TYPE.UNCALLED )
+                return false;
+        }
+        return true;
+    }
 
     public boolean equals(Object other) {
         if (other instanceof VCFGenotypeRecord) {