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

This commit is contained in:
Eric Banks 2012-09-20 14:14:58 -04:00
parent 1316b579f0 c492185be6
commit 747694f7c2
3 changed files with 58 additions and 5 deletions
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22
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
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@ -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;

36
public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
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@ -30,16 +30,26 @@ public class MannWhitneyU {
private int sizeSet2;
private ExactMode exactMode;
public MannWhitneyU() {
observations = new TreeSet<Pair<Number,USet>>(new DitheringComparator());
public MannWhitneyU(ExactMode mode, boolean dither) {
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();
exactMode = mode;
this(mode,true);
}
/**
@ -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 }

5
public/java/test/org/broadinstitute/sting/utils/MWUnitTest.java
View File

@ -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();