gatk3的最后一个经典版本3.8

Eric Banks 35fc2e13c3 Using the new PL cache, fix a bug: when only a subset of the genotyped alleles are used for assigning genotypes (because the exact model determined that they weren't all real) the PLs need to be adjusted to reflect this. While fixing this I discovered that the integration tests are busted because ref calls (ALT=.) were getting annotated with PLs, which makes no sense at all.		2011-12-14 15:31:09 -05:00
public	Using the new PL cache, fix a bug: when only a subset of the genotyped alleles are used for assigning genotypes (because the exact model determined that they weren't all real) the PLs need to be adjusted to reflect this. While fixing this I discovered that the integration tests are busted because ref calls (ALT=.) were getting annotated with PLs, which makes no sense at all.	2011-12-14 15:31:09 -05:00
settings	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Extensive unit test for GenotypeContextUnitTest	2011-11-20 18:28:01 -05:00
ivy.xml	Updating the HybridSelectionPipeline for SnpEff 2.0.4 RC3	2011-11-17 14:46:12 -05:00