updates to be compatible with Java 7

broadinstitute · Aug 16, 2013 · f07a1d1 · f07a1d1
1 parent 85cb5a1
commit f07a1d1
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Showing 2 changed files with 57 additions and 10 deletions.
diff --git a/src/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTect.java b/src/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTect.java
@@ -140,23 +140,36 @@ public enum SampleType {TUMOR, NORMAL}
     private NormalPowerCalculator normalDbSNPSitePowerCalculator;
     private TumorPowerCalculator strandArtifactPowerCalculator;
 
-    private static class PileupComparatorByAltRefQual implements Comparator<PileupElement> {
+    public static class PileupComparatorByAltRefQual implements Comparator<PileupElement> {
         private byte alt;
 
-        private PileupComparatorByAltRefQual(byte alt) {
+        public PileupComparatorByAltRefQual(byte alt) {
             this.alt = alt;
         }
 
         public int compare(PileupElement o1, PileupElement o2) {
+            return internalCompare(o1.getBase(), o1.getQual(), o2.getBase(), o2.getQual());
+        }
+
+        public int internalCompare(byte base1, byte qual1, byte base2, byte qual2) {
             // if the bases are the same, the higher quality score comes first
-            if (o1.getBase() ==  o2.getBase()) {
-                if (o1.getQual() == o2.getQual()) { return 0; }
-                return (o1.getQual() > o2.getQual())?-1:1;
+            if (base1 == base2) {
+                if (qual1 == qual2) { return 0; }
+                return (qual1 > qual2)?-1:1;
+
+            // if the bases are not the same, then the alternate is first
             } else {
-                return (o1.getBase() == alt)?-1:1;
-            }
+                if (base1 == alt) {
+                    return -1;
+                } else if (base2 == alt) {
+                    return 1;
+                } else {
+                    return base1 < base2?-1:1;
+                }
 
+            }
         }
+
     }
 
 
@@ -729,7 +742,6 @@ protected Map<SampleType, ReadBackedPileup> getPileupsBySampleType(ReadBackedPil
         ArrayList<PileupElement> normalPileupElements = new ArrayList<PileupElement>();
 
         for (PileupElement p : pileup ) {
-            final GATKSAMRecord read = p.getRead();
             final byte base = p.getBase();
 
             if (base == ((byte)'N') || base == ((byte)'n')) {

diff --git a/test/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTectWalkerUnitTest.java b/test/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTectWalkerUnitTest.java
@@ -91,8 +91,8 @@ public void simulate() {
 
         final int trials = 100; // set to 10,000 for paper
 
-        final Integer[] depths = new Integer[]{5,10,15,20,25,30,35,40,45,50};
-        final Double[] trueAlleleFractions = new Double[]{0.1, 0.2, 0.4};
+        final Integer[] depths = new Integer[]{0, 5,10,15,20,25,30,35,40,45,50};
+        final Double[] trueAlleleFractions = new Double[]{0.1, 0.2, 0.4, 0.5};
 
         ReferenceContext refContext = new ReferenceContext(genomeLocParser, loc, (byte)ref);
         Random r = new Random();
@@ -207,6 +207,41 @@ public static ReadBackedPileup createReadBackedPileup(final SAMFileHeader header
         return new ReadBackedPileupImpl(loc, pileupElements);
     }
 
+    @Test
+    public void testPileupComparator() {
+        byte A = (byte) 'A';
+        byte C = (byte) 'C';
+        byte T = (byte) 'T';
+        byte Q30 = (byte) 30;
+        byte Q60 = (byte) 60;
+
+        MuTect.PileupComparatorByAltRefQual c = new MuTect.PileupComparatorByAltRefQual(A);
+
+        // recall:
+        //      A<B -> -1
+        //      A=B ->  0
+        //      A>B ->  1
+        Assert.assertEquals(c.internalCompare(A, Q30, A, Q60), 1);
+        Assert.assertEquals(c.internalCompare(A, Q60, A, Q30), -1);
+        Assert.assertEquals(c.internalCompare(A, Q60, A, Q60), 0);
+
+        Assert.assertEquals(c.internalCompare(C, Q30, C, Q60), 1);
+        Assert.assertEquals(c.internalCompare(C, Q60, C, Q30), -1);
+        Assert.assertEquals(c.internalCompare(C, Q60, C, Q60), 0);
+
+        Assert.assertEquals(c.internalCompare(A, Q30, C, Q60), -1);
+        Assert.assertEquals(c.internalCompare(A, Q60, C, Q30), -1);
+        Assert.assertEquals(c.internalCompare(A, Q60, C, Q60), -1);
+
+        Assert.assertEquals(c.internalCompare(C, Q30, A, Q60), 1);
+        Assert.assertEquals(c.internalCompare(C, Q60, A, Q30), 1);
+        Assert.assertEquals(c.internalCompare(C, Q60, A, Q60), 1);
+
+        Assert.assertEquals(c.internalCompare(C, Q60, T, Q60), -1);
+        Assert.assertEquals(c.internalCompare(T, Q60, C, Q60), 1);
+
+    }
+
     public static int getBinomial(int n, double p) {
         int x = 0;
         for(int i = 0; i < n; i++) {