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Adding ReadPos rank sum test. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5560 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2011-04-02 22:28:41 +00:00
parent 09e89c8c97
commit 98798eb276
1 changed files with 41 additions and 0 deletions
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41
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java 100755
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package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import java.util.Arrays;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: rpoplin
* Date: 3/30/11
*/
public class ReadPosRankSumTest extends RankSumTest {
public List<String> getKeyNames() { return Arrays.asList("ReadPosRankSum"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref read position bias")); }
protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Integer> refQuals, List<Integer> altQuals) {
for ( final PileupElement p : pileup ) {
if( isUsableBase(p) ) {
int readPos = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p.getOffset(), 0, 0);
final int numAlignedBases = AlignmentUtils.getNumAlignedBases(p.getRead());
if( readPos > numAlignedBases / 2 ) {
readPos = numAlignedBases - ( readPos + 1 );
}
if ( p.getBase() == ref ) {
refQuals.add( readPos );
} else if ( p.getBase() == alt ) {
altQuals.add( readPos );
}
}
}
}
}