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Removed secondary-base test from SingleSampleGenotyper. It now lives in the variant filtration system. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1302 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-07-23 20:58:41 +00:00
parent 477502338f
commit 093550a3f2
1 changed files with 10 additions and 4 deletions
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14
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -24,6 +24,7 @@ import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.List;
import java.util.ArrayList;
@ReadFilters(ZeroMappingQualityReadFilter.class)
public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate, String> {
@ -42,7 +43,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
@Argument(fullName = "suppress_metrics", shortName = "printmets", doc = "If specified, don't display metrics", required = false) public Boolean SUPPRESS_METRICS = false;
// Control what features we use in calling variants
@Argument(fullName = "ignore_secondary_bases", shortName = "nosb", doc = "Ignore secondary base examination", required = false) public Boolean IGNORE_SECONDARY_BASES = false;
//@Argument(fullName = "ignore_secondary_bases", shortName = "nosb", doc = "Ignore secondary base examination", required = false) public Boolean IGNORE_SECONDARY_BASES = false;
@Argument(fullName = "call_indels", shortName = "indels", doc = "Call indels as well as point mutations", required = false) public Boolean CALL_INDELS = false;
// Control how the genotype hypotheses are weighed
@ -203,9 +204,11 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
// Handle indels, but don't do anything with the result yet.
IndelLikelihood I = (CALL_INDELS) ? callIndel(context, reads, offsets) : null;
//IndelLikelihood I = (CALL_INDELS) ? callIndel(context, context.getReads(), context.getOffsets()) : null;
// Handle single-base polymorphisms.
GenotypeLikelihoods G = callGenotype(tracker, ref, pileup, reads, offsets);
//GenotypeLikelihoods G = callGenotype(tracker, ref, context);
return G.toAlleleFrequencyEstimate(context.getLocation(), ref, bases.length(), bases, G.likelihoods, sample_name);
}
@ -240,9 +243,12 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
}
G.ApplyPrior(ref, this.alt_allele, this.allele_frequency_prior);
if (!IGNORE_SECONDARY_BASES && pileup.getBases().length() < 750) {
G.applySecondBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
}
//if (!IGNORE_SECONDARY_BASES && pileup.getBases().length() < 750) {
// G.applySecondBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
//}
G.applySecondBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
return G;
}