Changes:

Rollback of Variant-related changes of r1585, additional PGC code




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1586 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -145,8 +145,4 @@ public interface AllelicVariant extends ReferenceOrderedDatum {
      */
     int length();
 
-    /**
-     * returns TRUE if the variant is one for pooled calls, FALSE if it is not
-     */
-    boolean isPooled();
 }

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

@@ -46,7 +46,6 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
     public int length() { return 1; }
-    public boolean isPooled() { return true; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return Integer.parseInt(this.get("EM_N")); }

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

@@ -408,9 +408,5 @@ public class RodGLF implements ReferenceOrderedDatum, AllelicVariant, Iterator<R
         return glf;
     }
 
-    @Override
-    public boolean isPooled() {
-        return false;
-    }
 }
 

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

@@ -171,7 +171,6 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements AllelicVa
         return true;
     }
 
-    public boolean isPooled() { return false; }
 
     public int length() { return 1; }
 

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

@@ -175,5 +175,4 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic() { return true; }
     public int length() { return 1; }
-    public boolean isPooled() { return false; }
 }

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

@@ -32,7 +32,6 @@ public class SangerSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
     public int length() { return 1; }
-    public boolean isPooled() { return false; }
 
     // SNPCallFromGenotypes interface
     public int nIndividuals()      { return -1; }

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

@@ -58,7 +58,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
     public double getHeterozygosity() { return 0.0; }
     public double getMAF() { return 0.0; }
     public int getPloidy() { return 2; }
-    public boolean isPooled() { return false; }
     public int length() {
         if ( is1KGFormat() )
              return Integer.parseInt(this.get("2"));

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

@@ -240,5 +240,4 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 
     public int length() { return (int)(loc.getStop() - loc.getStart() + 1); }
 
-    public boolean isPooled() { return false; }
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java

@@ -80,7 +80,23 @@ public class PooledGenotypeConcordance extends BasicVariantAnalysis implements G
 
     public void inc(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context, int pool, int nameOffset) {
         AllelicVariant chip = (AllelicVariant) tracker.lookup(individualsByPool[pool][nameOffset],null);
+        if( (chip != null && !chip.isGenotype()) || ! isCorrectVariantType(eval)) {
+            String errMsg = "Trying to compare non-pooled data or non-genotype data."
+            throw new StingException(errMsg);
+        }
 
+        int truthIndex, callIndex;
+        if(chip == null) {
+            truthIndex = UNKNOWN;
+        } else if(chip.isReference()) // todo -- how do we want to do pooled concordance checking?
+
+    }
+
+    public boolean isCorrectVariantType(AllelicVariant eval) {
+        // todo -- this. Check if eval is a TypeOf some ROD class that's the right pooled call output that we
+        // todo -- want to deal with. For now this will work
+
+        return eval.isPooled();
     }