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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 ("./.").
This commit is contained in:
Christopher Hartl 2012-01-26 12:43:52 -05:00
parent 9d4b84f6bd
commit 7d059540a4
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
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@ -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);