gatk3的最后一个经典版本3.8

Guillermo del Angel 4308b27f8c Fixed non-determinism in HaplotypeCaller and some UG calls - ... -- HaplotypeCaller and PerReadAlleleLikelihoodMap should use LinkedHashMaps instead of plain HashMaps. That way the ordering when traversing alleles is maintained. If the JVM traverses HashMaps with random ordering, different reads (with same likelihood) may be removed by contamination checker, and different alleles may be picked if they have same likelihoods for all reads. -- Put in some GATKDocs and contracts in HaplotypeCaller files (far from done, code is a beast) -- Update md5's due to different order of iteration in LinkedHashMaps instead of HashMaps inside HaplotypeCaller (due to change in PerReadAlleleLikelihoodMap that also slightly modifies reads chosen by per-read downsampling). -- Reenabled testHaplotypeCallerMultiSampleGGAMultiAllelic test -- Added some defensive argument checks into HaplotypeCaller public functions (not intended to be done yet).		2013-02-12 15:43:29 -05:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected/java	Fixed non-determinism in HaplotypeCaller and some UG calls -	2013-02-12 15:43:29 -05:00
public	Fixed non-determinism in HaplotypeCaller and some UG calls -	2013-02-12 15:43:29 -05:00
settings	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Minor build.xml cleanup post-variant-migration	2013-02-06 11:16:52 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00