Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java

@@ -21,7 +21,7 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * Variant confidence (given as (AB+BB)/AA from the PLs) / unfiltered depth.
+ * Variant confidence (from the QUAL field) / unfiltered depth.
  *
  * Low scores are indicative of false positive calls and artifacts.  Note that QualByDepth requires sequencing
  * reads associated with the samples with polymorphic genotypes.

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java

@@ -253,14 +253,14 @@ public class ConsensusAlleleCounter {
                 stop = loc.getStart() + dLen;
                 final byte[] refBases = Arrays.copyOfRange(ref.getBases(), startIdxInReference, startIdxInReference + dLen);
 
-                if (Allele.acceptableAlleleBases(refBases)) {
+                if (Allele.acceptableAlleleBases(refBases, false)) {
                     refAllele = Allele.create(refBases, true);
                     altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
                 }
                 else continue; // don't go on with this allele if refBases are non-standard
             } else {
                 // insertion case
-                if (Allele.acceptableAlleleBases(s)) {
+                if (Allele.acceptableAlleleBases(s, false)) { // don't allow N's in insertions
                     refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true);
                     altAllele = Allele.create(s, false);
                     stop = loc.getStart();

public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java

@@ -226,7 +226,11 @@ public class Allele implements Comparable<Allele> {
      * @return true if the bases represent the well formatted allele
      */
     public static boolean acceptableAlleleBases(String bases) {
-        return acceptableAlleleBases(bases.getBytes());
+        return acceptableAlleleBases(bases.getBytes(), true);
+    }
+
+    public static boolean acceptableAlleleBases(String bases, boolean allowNsAsAcceptable) {
+        return acceptableAlleleBases(bases.getBytes(), allowNsAsAcceptable);
     }
 
     /**
@@ -234,13 +238,22 @@ public class Allele implements Comparable<Allele> {
      * @return true if the bases represent the well formatted allele
      */
     public static boolean acceptableAlleleBases(byte[] bases) {
+        return acceptableAlleleBases(bases, true); // default: N bases are acceptable
+    }
+    
+    public static boolean acceptableAlleleBases(byte[] bases, boolean allowNsAsAcceptable) {
         if ( wouldBeNullAllele(bases) || wouldBeNoCallAllele(bases) || wouldBeSymbolicAllele(bases) )
             return true;
 
-        for ( int i = 0; i < bases.length; i++ ) {
+        for (byte base :  bases ) {
-            switch (bases[i]) {
+            switch (base) {
-                case 'A': case 'C': case 'G': case 'T': case 'N' : case 'a': case 'c': case 'g': case 't': case 'n' :
+                case 'A': case 'C': case 'G': case 'T':  case 'a': case 'c': case 'g': case 't': 
                     break;
+                case 'N' : case 'n' :
+                    if (allowNsAsAcceptable)
+                        break;
+                    else
+                        return false;
                 default:
                     return false;
             }

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java

@@ -90,6 +90,21 @@ public class IndelGenotypeLikelihoodsUnitTest extends BaseTest {
         Assert.assertEquals(alleles.size(),2);
         alleles = getConsensusAlleles(eventLength,false,10,0.5001, altBases);
         Assert.assertEquals(alleles.size(),0);
+
+        // test N's in insertions
+        altBases = "CCTCNTGAGA";
+        eventLength = 4;
+        alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases);
+
+        Assert.assertEquals(alleles.size(),2);
+        Assert.assertEquals(alleles.get(1).getBaseString(), altBases.substring(0,eventLength));
+
+        altBases = "CCTCNTGAGA";
+        eventLength = 5;
+        alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases);
+
+        Assert.assertEquals(alleles.size(),0);
+
     }
     
     private List<Allele> getConsensusAlleles(int eventLength, boolean isInsertion, int minCnt, double minFraction, String altBases) {