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Now aware of Hapmap and dbSNP sites. We *can* change the priors there, but we don't yet. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@993 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-11 21:15:34 +00:00
parent d5cd883b99
commit 12dd18cdba
1 changed files with 26 additions and 4 deletions
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30
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -80,11 +80,10 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
} }
} }
AlleleFrequencyEstimate freq = getAlleleFrequency(ref, context, sample_name); AlleleFrequencyEstimate freq = getAlleleFrequency(tracker, ref, context, sample_name);
if (printMetrics) { if (printMetrics) {
if (freq != null) { if (freq != null) {
//System.out.println(context.getContig() + ":" + context.getPosition());
metrics.nextPosition(freq, tracker); metrics.nextPosition(freq, tracker);
} }
metrics.printMetricsAtLocusIntervals(metricsInterval); metrics.printMetricsAtLocusIntervals(metricsInterval);
@ -93,7 +92,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
return freq; return freq;
} }
private AlleleFrequencyEstimate getAlleleFrequency(char ref, LocusContext context, String sample_name) { private AlleleFrequencyEstimate getAlleleFrequency(RefMetaDataTracker tracker, char ref, LocusContext context, String sample_name) {
ReadBackedPileup pileup = new ReadBackedPileup(ref, context); ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
String bases = pileup.getBases(); String bases = pileup.getBases();
@ -123,7 +122,22 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
// Handle single-base polymorphisms. // Handle single-base polymorphisms.
GenotypeLikelihoods G = new GenotypeLikelihoods(PRIOR_HOM_REF, PRIOR_HET, PRIOR_HOM_VAR); GenotypeLikelihoods G = new GenotypeLikelihoods(PRIOR_HOM_REF, PRIOR_HET, PRIOR_HOM_VAR);
for ( int i = 0; i < reads.size(); i++ )
if (isHapmapSite(tracker)) {
//System.out.println(context.getLocation() + " is a Hapmap site.");
//G.setHomRefPrior(PRIOR_HOM_REF);
//G.setHetPrior(PRIOR_HET);
//G.setHomVarPrior(PRIOR_HOM_VAR);
} else if (isDbSNPSite(tracker)) {
//System.out.println(context.getLocation() + " is a dbSNP site.");
//G.setHomRefPrior(PRIOR_HOM_REF);
//G.setHetPrior(PRIOR_HET);
//G.setHomVarPrior(PRIOR_HOM_VAR);
}
for ( int i = 0; i < reads.size(); i++ )
{ {
SAMRecord read = reads.get(i); SAMRecord read = reads.get(i);
int offset = offsets.get(i); int offset = offsets.get(i);
@ -139,6 +153,14 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
return G.toAlleleFrequencyEstimate(context.getLocation(), ref, bases.length(), bases, G.likelihoods, sample_name); return G.toAlleleFrequencyEstimate(context.getLocation(), ref, bases.length(), bases, G.likelihoods, sample_name);
} }
private boolean isHapmapSite(RefMetaDataTracker tracker) {
return tracker.lookup("hapmap-chip", null) != null;
}
private boolean isDbSNPSite(RefMetaDataTracker tracker) {
return tracker.lookup("dbsnp", null) != null;
}
private String getRodString(RefMetaDataTracker tracker) { private String getRodString(RefMetaDataTracker tracker) {
String rodString = ""; String rodString = "";