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After a minor and abject freakout, alter the T2D script to seek out truth sensitivities between 80 and 100, rather than between 0.8 and 1. Also, don't consider a genotype "changed by beagle" if the initial genotype is a no-call.

This commit is contained in:
Christopher Hartl 2012-01-20 23:43:51 -05:00
parent 9b4f6afa21
commit 3b1aad4f17
1 changed files with 6 additions and 2 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -320,8 +320,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
og = a1+"/"+a2; og = a1+"/"+a2;
// See if Beagle switched genotypes // See if Beagle switched genotypes
if (!((bglAlleleA.equals(originalAlleleA) && bglAlleleB.equals(originalAlleleB) || if (! originalAlleleA.equals(Allele.NO_CALL) && beagleSwitchedGenotypes(bglAlleleA,originalAlleleA,bglAlleleB,originalAlleleB)){
(bglAlleleA.equals(originalAlleleB) && bglAlleleB.equals(originalAlleleA))))){
originalAttributes.put("OG",og); originalAttributes.put("OG",og);
numGenotypesChangedByBeagle++; numGenotypesChangedByBeagle++;
} }
@ -364,6 +363,11 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
return 1; return 1;
} }
private boolean beagleSwitchedGenotypes(Allele bglAlleleA, Allele originalAlleleA, Allele bglAlleleB, Allele originalAlleleB) {
return !((bglAlleleA.equals(originalAlleleA) && bglAlleleB.equals(originalAlleleB) ||
(bglAlleleA.equals(originalAlleleB) && bglAlleleB.equals(originalAlleleA))));
}
public Integer reduceInit() { public Integer reduceInit() {
return 0; // Nothing to do here return 0; // Nothing to do here
} }