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bug fixes

This commit is contained in:
Guillermo del Angel 2011-07-04 21:04:49 -04:00
parent f26ffeaea0
commit bb85f232b9
1 changed files with 42 additions and 47 deletions
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89
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -265,7 +265,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
}
}
}
}
/**
* Subset VC record if necessary and emit the modified record (provided it satisfies criteria for printing)
@ -326,58 +326,53 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
}
else {
if (SELECT_RANDOM_FRACTION && KEEP_AF_SPECTRUM ) {
Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, inputAFRodName, null, context.getLocation(), true, false);
if (compVCs.isEmpty())
return 0;
// ok we have a comp VC and we need to match the AF spectrum of inputAFRodName.
// We then pick a variant with probablity AF*desiredFraction
for (VariantContext compVC : compVCs) {
if ( compVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
String afo = compVC.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY);
double af;
double afBoost = 1.0;
if (afo.contains(",")) {
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);
if ( sub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
String afo = sub.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY);
double[] afd = new double[afs.length];
double af;
double afBoost = 1.0;
if (afo.contains(",")) {
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);
for (int k=0; k < afd.length; k++)
afd[k] = Double.valueOf(afs[k]);
double[] afd = new double[afs.length];
af = MathUtils.arrayMax(afd);
//af = Double.valueOf(afs[0]);
for (int k=0; k < afd.length; k++)
afd[k] = Double.valueOf(afs[k]);
}
else
af = Double.valueOf(afo);
af = MathUtils.arrayMax(afd);
//af = Double.valueOf(afs[0]);
// now boost af by table read from file if desired
//double bkpt = 0.0;
int bkidx = 0;
if (AF_FILE != null) {
for ( Double bkpt : afBreakpoints) {
if (af < bkpt + bkDelta)
break;
else bkidx++;
}
afBoost = afBreakpoints.get(bkidx);
System.out.format("af:%f bkidx:%d afboost:%f\n",af,bkidx,afBoost);
}
//System.out.format("%s .. %4.4f\n",afo.toString(), af);
if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * af * afBoost)
vcfWriter.add(sub, ref.getBase());
}
break; // do only one vc
else
af = Double.valueOf(afo);
// now boost af by table read from file if desired
//double bkpt = 0.0;
int bkidx = 0;
if (AF_FILE != null) {
for ( Double bkpt : afBreakpoints) {
if (af < bkpt + bkDelta)
break;
else bkidx++;
}
afBoost = afBreakpoints.get(bkidx);
System.out.format("af:%f bkidx:%d afboost:%f\n",af,bkidx,afBoost);
}
//System.out.format("%s .. %4.4f\n",afo.toString(), af);
if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * af * afBoost)
vcfWriter.add(sub, ref.getBase());
}
}
}
}
@ -461,8 +456,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
private boolean haveSameGenotypes(Genotype g1, Genotype g2) {
if ((g1.isCalled() && g2.isFiltered()) ||
(g2.isCalled() && g1.isFiltered()) ||
(g1.isFiltered() && g2.isFiltered() && EXCLUDE_FILTERED))
(g2.isCalled() && g1.isFiltered()) ||
(g1.isFiltered() && g2.isFiltered() && EXCLUDE_FILTERED))
return false;
List<Allele> a1s = g1.getAlleles();
@ -495,7 +490,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
* @param vc the VariantContext record to subset
* @param samples the samples to extract
* @return the subsetted VariantContext
*/
*/
private VariantContext subsetRecord(VariantContext vc, Set<String> samples) {
if ( samples == null || samples.isEmpty() )
return vc;
@ -505,7 +500,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if ( samples.contains(genotypePair.getKey()) )
genotypes.add(genotypePair.getValue());
}
VariantContext sub = vc.subContextFromGenotypes(genotypes, vc.getAlleles());
HashMap<String, Object> attributes = new HashMap<String, Object>(sub.getAttributes());
@ -515,7 +510,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
Genotype g = sub.getGenotype(sample);
if (g.isNotFiltered() && g.isCalled()) {
String dp = (String) g.getAttribute("DP");
if (dp != null && ! dp.equals(VCFConstants.MISSING_DEPTH_v3) && ! dp.equals(VCFConstants.MISSING_VALUE_v4) ) {
depth += Integer.valueOf(dp);