diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java new file mode 100755 index 000000000..351117809 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java @@ -0,0 +1,77 @@ +package org.broadinstitute.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.IndelUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.*; + +/** + * Created by IntelliJ IDEA. + * User: delangel + * Date: 6/29/11 + * Time: 3:14 PM + * To change this template use File | Settings | File Templates. + */ +public class TechnologyComposition implements ExperimentalAnnotation,InfoFieldAnnotation { + private String nSLX = "NumSLX"; + private String n454 ="Num454"; + private String nSolid = "NumSOLiD"; + private String nOther = "NumOther"; + public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + if ( stratifiedContexts.size() == 0 ) + return null; + + int readsIllumina = 0; + int readsSolid = 0; + int reads454 = 0; + int readsOther = 0; + + for ( Map.Entry sample : stratifiedContexts.entrySet() ) { + AlignmentContext context = sample.getValue(); + + ReadBackedPileup pileup = null; + if (context.hasExtendedEventPileup()) + pileup = context.getExtendedEventPileup(); + else if (context.hasBasePileup()) + pileup = context.getBasePileup(); + + if (pileup != null) { + for (PileupElement p : pileup ) { + if(ReadUtils.is454Read(p.getRead())) + reads454++; + else if (ReadUtils.isSOLiDRead(p.getRead())) + readsSolid++; + else if (ReadUtils.isSLXRead(p.getRead())) + readsIllumina++; + else + readsOther++; + } + } + } + + Map map = new HashMap(); + map.put(nSLX, String.format("%d", readsIllumina)); + map.put(n454, String.format("%d", reads454)); + map.put(nSolid, String.format("%d", readsSolid)); + map.put(nOther, String.format("%d", readsOther)); + return map; + } + + public List getKeyNames() { return Arrays.asList(nSLX,n454,nSolid,nOther); } + + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(nSLX, 1, VCFHeaderLineType.Integer, "Number of SLX reads"), + new VCFInfoHeaderLine(n454, 1, VCFHeaderLineType.Integer, "Number of 454 reads"), + new VCFInfoHeaderLine(nSolid, 1, VCFHeaderLineType.Integer, "Number of SOLiD reads"), + new VCFInfoHeaderLine(nOther, 1, VCFHeaderLineType.Integer, "Number of Other technology reads")); } + +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 4916c4ac4..cbac54326 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; @@ -303,13 +304,20 @@ public class SelectVariants extends RodWalker { String[] afs = afo.split(","); afs[0] = afs[0].substring(1,afs[0].length()); afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1); - af = Double.valueOf(afs[0]); + + double[] afd = new double[afs.length]; + + for (int k=0; k < afd.length; k++) + afd[k] = Double.valueOf(afs[k]); + + af = MathUtils.arrayMax(afd); + //af = Double.valueOf(afs[0]); } else af = Double.valueOf(afo); - System.out.format("%s .. %4.1f\n",afo.toString(), af); + //System.out.format("%s .. %4.4f\n",afo.toString(), af); if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * af) vcfWriter.add(sub, ref.getBase()); }