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kcibul
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package org.broadinstitute.sting.playground.gatk.walkers.cancer;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
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import org.broadinstitute.sting.gatk.LocusContext;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
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import java.util.Map;
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import java.util.HashMap;
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import java.util.List;
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import net.sf.samtools.SAMRecord;
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/**
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* Created by IntelliJ IDEA.
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* User: kcibul
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* Date: Jun 27, 2009
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* Time: 3:21:23 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class LOHWalker extends LocusWalker<Integer, Integer> {
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@Argument(fullName = "tumor_sample_name", shortName = "s1", required = true, doc="Name of the tumor sample")
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public String tumorSampleName;
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@Argument(fullName = "normal_sample_name", shortName = "s2", required = true, doc="Name of the normal sample")
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public String normalSampleName;
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public Integer reduceInit() {
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return null; //To change body of implemented methods use File | Settings | File Templates.
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}
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public Integer reduce(Integer value, Integer sum) {
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return null; //To change body of implemented methods use File | Settings | File Templates.
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}
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@Override
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public void initialize() {
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out.println("chrom\tposition\tnormal_btnb\tallele1\tallele2\tnormal_allele1_count\tnormal_allele2_count\tnormal_mar\ttumor_allele1_count\ttumor_allele2_count\ttumor_mar");
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}
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public static int MAX_INSERT_SIZE = 10000;
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public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
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char upRef = Character.toUpperCase(ref);
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// TODO: should we be able to call mutations at bases where ref is N?
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if (upRef == 'N') { return -1; }
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List<SAMRecord> reads = context.getReads();
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LocusReadPile tumorReadPile = new LocusReadPile(upRef);
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LocusReadPile normalReadPile = new LocusReadPile(upRef);
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for ( int i = 0; i < reads.size(); i++ )
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{
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SAMRecord read = reads.get(i);
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if (read.getNotPrimaryAlignmentFlag() ||
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read.getDuplicateReadFlag() ||
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read.getReadUnmappedFlag() ||
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read.getMappingQuality() <= 0
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// || (read.getReadPairedFlag() && (!read.getProperPairFlag() || read.getInferredInsertSize() >= MAX_INSERT_SIZE))
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) {
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continue;
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}
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String rg = (String) read.getAttribute("RG");
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String sample = read.getHeader().getReadGroup(rg).getSample();
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int offset = context.getOffsets().get(i);
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char base = read.getReadString().charAt(offset);
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if (base == 'N' || base == 'n') { continue; }
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// TODO: build a pile of reads and offsets, then pass that into a
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// constructor for the normalGL class
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// that way, we can build a different pile of reads later on and extract the genotype
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if (normalSampleName.equals(sample)) {
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normalReadPile.add(read, offset);
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} else if (tumorSampleName.equals(sample)) {
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tumorReadPile.add(read, offset);
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} else {
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throw new RuntimeException("Unknown Sample Name: " + sample);
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}
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}
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normalReadPile.likelihoods.ApplyPrior(upRef,' ', -1); // apply std priors
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double normalBtnb = normalReadPile.likelihoods.LodVsNextBest();
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if (normalBtnb < 5.0) { return null; }
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String normalGt = normalReadPile.likelihoods.BestGenotype();
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char allele1 = normalGt.charAt(0);
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char allele2 = normalGt.charAt(1);
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if (allele2 == upRef) {
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char oldAllele1 = allele1;
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allele1 = allele2;
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allele2 = oldAllele1;
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}
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if (allele1 == upRef && allele1 == allele2) {
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return null;
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}
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StringBuilder sb = new StringBuilder();
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sb.append(String.format("%s\t%d\t%1.2f\t%s\t%s\t",
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context.getContig(),
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context.getPosition(),
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normalBtnb,
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allele1,
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allele2));
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int normalAllele1Counts = normalReadPile.qualitySums.getCounts(allele1);
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int normalAllele2Counts = normalReadPile.qualitySums.getCounts(allele2);
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int tumorAllele1Counts = tumorReadPile.qualitySums.getCounts(allele1);
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int tumorAllele2Counts = tumorReadPile.qualitySums.getCounts(allele2);
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// allele ratio in the normal
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double normalAlleleRatio =
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(double) normalAllele2Counts / (double) (normalAllele1Counts+normalAllele2Counts) ;
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// allele ratio in the tumor
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double tumorAlleleRatio =
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(double) tumorAllele2Counts / (double) (tumorAllele1Counts+tumorAllele2Counts) ;
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sb.append(
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String.format("%d\t%d\t%1.2f\t%d\t%d\t%1.2f",
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normalAllele1Counts,
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normalAllele2Counts,
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normalAlleleRatio,
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tumorAllele1Counts,
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tumorAllele2Counts,
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tumorAlleleRatio));
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// // do the normal
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// for (char allele : new char[]{'A','C','G','T'}) {
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// QualitySums qs = normalReadPile.qualitySums;
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// sb.append(" ");
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// sb.append(qs.getCounts(allele)).append(" ");
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//// sb.append(qs.getQualitySum(allele));
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// }
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//
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// // do the tumor
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// for (char allele : new char[]{'A','C','G','T'}) {
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// QualitySums qs = tumorReadPile.qualitySums;
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// sb.append(" ");
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// sb.append(qs.getCounts(allele)).append(" ");
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//// sb.append(qs.getQualitySum(allele));
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// }
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out.println(sb);
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return null;
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}
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}
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@ -32,6 +32,10 @@ public class LocusReadPile {
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}
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public void add(SAMRecord read, int offset) {
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add(read, offset, false);
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}
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public void add(SAMRecord read, int offset, boolean allowMapq0ForQualSum) {
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char base = read.getReadString().charAt(offset);
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byte qual = read.getBaseQualities()[offset];
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@ -42,8 +46,10 @@ public class LocusReadPile {
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likelihoods.add(refBase, base, qual);
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if (qual > this.minQualityScore) qualitySums.incrementSum(base, qual);
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if (read.getMappingQuality() == 0 && !allowMapq0ForQualSum) { return; }
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if (qual > this.minQualityScore) qualitySums.incrementSum(base, qual);
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}
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public String getLocusBases() {
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@ -50,8 +50,10 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
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@Argument(fullName = "output_failures", required = false, doc="produce output for failed sites")
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public boolean OUTPUT_FAILURES = false;
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@Argument(fullName="maf_file", shortName="stats", doc="write out calls in MAF format to this file", required=false)
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String MAF_FILE = null;
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@Argument(fullName="maf_file", shortName="maf", doc="write out calls in MAF format to this file", required=false)
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public String MAF_FILE = null;
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public boolean USE_MAPQ0_IN_NORMAL_QSCORE = true;
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private FileWriter mafWriter = null;
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@ -115,9 +117,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
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if (read.getNotPrimaryAlignmentFlag() ||
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read.getDuplicateReadFlag() ||
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read.getReadUnmappedFlag() ||
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read.getMappingQuality() <= 0
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read.getReadUnmappedFlag()
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|| (read.getReadPairedFlag() && (!read.getProperPairFlag() || read.getInferredInsertSize() >= MAX_INSERT_SIZE))
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) {
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continue;
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@ -136,11 +136,12 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
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// constructor for the normalGL class
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// that way, we can build a different pile of reads later on and extract the genotype
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if (normalSampleName.equals(sample)) {
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normalReadPile.add(read, offset);
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normalReadPile.add(read, offset, USE_MAPQ0_IN_NORMAL_QSCORE);
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} else if (tumorSampleName.equals(sample)) {
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tumorReadPile.add(read, offset);
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if (read.getMappingQuality() > 0) {
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tumorReadPile.add(read, offset);
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}
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int midDist = Math.abs((int)(read.getReadLength() / 2) - offset);
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if (midDist < midp.get(base)) { midp.put(base, midDist); }
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