Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java

@@ -37,6 +37,28 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
     @ArgumentCollection
     protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
 
+    /**
+     * The metaData file can take two formats, the first of which is the first 6 lines of the standard ped file. This
+     * is what Plink describes as a fam file. An example fam file is (note that there is no header):
+     *
+     * CEUTrio NA12878 NA12891 NA12892 2 -9
+     * CEUTrio NA12891 UNKN1 UNKN2 2 -9
+     * CEUTrio NA12892 UNKN3 UNKN4 1 -9
+     *
+     * where the entries are (FamilyID IndividualID DadID MomID Phenotype Sex)
+     *
+     * An alternate format is a two-column key-value file
+     *
+     * NA12878        fid=CEUTrio;dad=NA12891;mom=NA12892;sex=2;phenotype=-9
+     * NA12891        fid=CEUTrio;sex=2;phenotype=-9
+     * NA12892        fid=CEUTrio;sex=1;phenotype=-9
+     *
+     * wherein unknown parents needn't be specified. The columns are the individual ID, and a list of key-value pairs.
+     *
+     * Regardless of which file is specified, the walker will output a .fam file alongside the bed file. If the
+     * command line has "-md [name].fam", the fam file will simply be copied. However, if a metadata file of the
+     * alternate format is passed by "-md [name].txt", the walker will construct a formatted .fam file from the data.
+     */
     @Input(shortName="m",fullName = "metaData",required=true,doc="Sample metadata file. You may specify a .fam file " +
             "(in which case it will be copied to the file you provide as fam output).")
     File metaDataFile;

public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java

@@ -30,16 +30,26 @@ public class MannWhitneyU {
     private int sizeSet2;
     private ExactMode exactMode;
 
-    public MannWhitneyU() {
+    public MannWhitneyU(ExactMode mode, boolean dither) {
-        observations = new TreeSet<Pair<Number,USet>>(new DitheringComparator());
+        if ( dither )
+            observations = new TreeSet<Pair<Number,USet>>(new DitheringComparator());
+        else
+            observations = new TreeSet<Pair<Number,USet>>(new NumberedPairComparator());
         sizeSet1 = 0;
         sizeSet2 = 0;
-        exactMode = ExactMode.POINT;
+        exactMode = mode;
+    }
+
+    public MannWhitneyU() {
+        this(ExactMode.POINT,true);
+    }
+
+    public MannWhitneyU(boolean dither) {
+        this(ExactMode.POINT,dither);
     }
 
     public MannWhitneyU(ExactMode mode) {
-        super();
+        this(mode,true);
-        exactMode = mode;
     }
 
     /**
@@ -451,6 +461,22 @@ public class MannWhitneyU {
         }
     }
 
+    /**
+     * A comparator that reaches into the pair and compares numbers without tie-braking.
+     */
+    private static class NumberedPairComparator implements Comparator<Pair<Number,USet>>, Serializable {
+
+        public NumberedPairComparator() {}
+
+        @Override
+        public boolean equals(Object other) { return false; }
+
+        @Override
+        public int compare(Pair<Number,USet> left, Pair<Number,USet> right ) {
+            return Double.compare(left.first.doubleValue(),right.first.doubleValue());
+        }
+    }
+
     public enum USet { SET1, SET2 }
     public enum ExactMode { POINT, CUMULATIVE }
 

public/java/test/org/broadinstitute/sting/utils/MWUnitTest.java

@@ -40,12 +40,15 @@ public class MWUnitTest extends BaseTest {
         Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwu.getObservations(),MannWhitneyU.USet.SET2),11L);
 
         MannWhitneyU mwu2 = new MannWhitneyU();
+        MannWhitneyU mwuNoDither = new MannWhitneyU(false);
         for ( int dp : new int[]{2,4,5,6,8} ) {
             mwu2.add(dp,MannWhitneyU.USet.SET1);
+            mwuNoDither.add(dp,MannWhitneyU.USet.SET1);
         }
 
         for ( int dp : new int[]{1,3,7,9,10,11,12,13} ) {
             mwu2.add(dp,MannWhitneyU.USet.SET2);
+            mwuNoDither.add(dp,MannWhitneyU.USet.SET2);
         }
 
         MannWhitneyU.ExactMode pm = MannWhitneyU.ExactMode.POINT;
@@ -54,6 +57,8 @@ public class MWUnitTest extends BaseTest {
         // tests using the hypothesis that set 2 dominates set 1 (U value = 10)
         Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwu2.getObservations(),MannWhitneyU.USet.SET1),10L);
         Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwu2.getObservations(),MannWhitneyU.USet.SET2),30L);
+        Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwuNoDither.getObservations(),MannWhitneyU.USet.SET1),10L);
+        Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwuNoDither.getObservations(),MannWhitneyU.USet.SET2),30L);
 
         Pair<Integer,Integer> sizes = mwu2.getSetSizes();