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Added debugging message 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4605 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-11-01 19:51:42 +00:00
parent 639ecdc931
commit 64599d1074
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
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@ -357,6 +357,7 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite
logger.debug("Unknown segregation of alleles [not phased] for " + samp + " at " + VariantContextUtils.getLocation(vc1) + ", " + VariantContextUtils.getLocation(vc2));
}
else if (gt1.isHomRef() || gt2.isHomRef()) {
logger.debug("gt1.isHomRef() || gt2.isHomRef() for " + samp + " at " + VariantContextUtils.getLocation(vc1) + ", " + VariantContextUtils.getLocation(vc2));
aas.eitherNotVariant++;
}
else { // BOTH gt1 and gt2 have at least one variant allele (so either hets, or homozygous variant):