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a) consensus goes to week queue 

b) New experimental TechnologyComposition annotation
c) SelectVariants fixes
This commit is contained in:
Guillermo del Angel 2011-06-29 16:00:23 -04:00
parent e91ae6b265
commit dc4f63a1a8
2 changed files with 87 additions and 2 deletions
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77
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java 100755
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@ -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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;
int readsIllumina = 0;
int readsSolid = 0;
int reads454 = 0;
int readsOther = 0;
for ( Map.Entry<String, AlignmentContext> 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<String, Object> map = new HashMap<String, Object>();
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<String> getKeyNames() { return Arrays.asList(nSLX,n454,nSolid,nOther); }
public List<VCFInfoHeaderLine> 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")); }
}

12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -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<Integer, Integer> {
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());
}