fixing VariantEvalWalkerIntegrationTest md5 sums, a couple comment changes, and a little bit of cleanup

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1690 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -176,7 +176,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
 
     public boolean isSNP() {
         if (this.getReference().length() == 1)
-            return (!bestGenotype.equals(this.getReference() + this.getReference()));
+            return (this.refBase != this.bestGenotype.charAt(0) || this.refBase != this.bestGenotype.charAt(1));
         return false;
     }
 
@@ -223,7 +223,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
     @Override
     public char getAlternativeBaseForSNP() {
         if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
-        // we know that if we're a SNP, the reference is a single base
+        // we know that if we're a SNP, the alt is a single base
         if (this.bestGenotype.toString().charAt(0) == getReference().charAt(0))
             return this.bestGenotype.toString().charAt(1);
         return this.bestGenotype.toString().charAt(0);
@@ -354,7 +354,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
      */
     @Override
     public Genotype getCalledGenotype() {
-        return new BasicGenotype(getLocation(), this.getAltBasesFWD(), refBase, lodBtnb);
+        return new BasicGenotype(getLocation(), bestGenotype, refBase, lodBtnb);
     }
 
     /**
@@ -365,7 +365,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
     @Override
     public List<Genotype> getGenotypes() {
         List<Genotype> ret = new ArrayList<Genotype>();
-        ret.add(new BasicGenotype(getLocation(), this.getAltBasesFWD(), refBase, lodBtnb));
+        ret.add(new BasicGenotype(getLocation(), bestGenotype, refBase, lodBtnb));
         return ret;
     }
 

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

@@ -2,10 +2,9 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
-import org.broadinstitute.sting.utils.genotype.Genotype;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -33,8 +32,8 @@ public class VariantCounter extends BasicVariantAnalysis implements GenotypeAnal
         nSNPs += eval == null ? 0 : 1;
 
         if ( this.getMaster().evalContainsGenotypes && eval != null ) {
-            List<Genotype> genotypes = ((VariantBackedByGenotype)eval).getGenotypes();
+            Genotype genotype = ((VariantBackedByGenotype)eval).getCalledGenotype();
-            if ( eval.isSNP() && eval.isBiallelic() && genotypes.get(0).isHet() ) {
+            if ( eval.isSNP() && eval.isBiallelic() && genotype.isHet() ) {
                 nHets++;
             }
         }

java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java

@@ -80,7 +80,6 @@ public class BasicGenotype implements Genotype {
     public boolean isHom() {
         if (mGenotype.length() < 1)
             return false;
-
         char base = mGenotype.charAt(0);
         for (char cur : mGenotype.toCharArray()) {
             if (base != cur) {
@@ -97,6 +96,8 @@ public class BasicGenotype implements Genotype {
      */
     @Override
     public boolean isHet() {
+        if (mGenotype.length() < 1)
+            return false;
         return !isHom();
     }
 

java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java

@@ -19,7 +19,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testEvalVariantROD() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("013d13d405f33b0fe4038f5aea087e7f");
+        md5.add("7d1f8ddbf2d2f721a0c6dc39c97b584c");
 
         /**
          * the above MD5 was calculated from running the following command:
@@ -50,7 +50,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testEvalVariantRODConfSix() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("422d94ab60a3db42b0a5dc9c254b78f4");
+        md5.add("27969a841874fc00d007b01ee008eb58");
 
         /**
          * the above MD5 was calculated from running the following command:
@@ -82,7 +82,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
      @Test
     public void testEvalVariantRODOutputViolations() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("8e613d57fd770ff04eb6531f583f4448");
+        md5.add("63940f8d977b15bb1bcc9223ebeacf43");
 
         /**
          * the above MD5 was calculated from running the following command:
@@ -114,7 +114,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testEvalGenotypeROD() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("d337f22057d2e9cfda03af3be70ce35a");
+        md5.add("c616348c1041157acd2715285c5b38b8");
         /**
          * the above MD5 was calculated after running the following command:
          *
@@ -148,7 +148,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testEvalMarksGenotypingExample() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("39ea64299cad44f816f033db54c8e622");
+        md5.add("004cdf0c3ca46744daf42645785acc28");
         /**
          * Run with the following commands:
          *