From 7d059540a4ae48303678b35caf7946478ea55e0e Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 26 Jan 2012 12:43:52 -0500 Subject: [PATCH] Allow segments of genome to be excluded in generating a reference panel. Occasionally targets would contain no variation (typically, in the middle of the centromere), which beagle doesn't particularly like, and errors out rather than producing empty output files. The best way to deal with these is to just exclude the regions on a second-pass, and the remaining bits will be gathered with no additional work. AllelePair is being mean and not telling me what genotype it sees when it finds a non-diploid genotype, but i suspect it's a no-call (".") rather than a no call ("./."). --- .../broadinstitute/sting/gatk/walkers/phasing/AllelePair.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java index cb123c868..c629bd313 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java @@ -36,7 +36,7 @@ public class AllelePair { public AllelePair(Genotype gt) { if (gt.getPloidy() != 2) - throw new ReviewedStingException("AllelePair must have ploidy of 2!"); + throw new ReviewedStingException("AllelePair must have ploidy of 2! incoming gt was"+gt.toBriefString()); this.top = gt.getAllele(0); this.bottom = gt.getAllele(1);