gatk3的最后一个经典版本3.8

Mark DePristo 29319bf222 Improved allele trimming code in GATKVariantContextUtils ... -- Now supports trimming the alleles from both the reverse and forward direction. -- Added lots of unit tests for forwrad allele trimming, as well as creating VC from forward and reverse trimming. -- Added docs and tests for the code, to bring it up to GATK spec		2013-02-21 12:01:43 -05:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected/java	Haplotype/Allele based optimizations for the HaplotypeCaller that knock off nearly 20% of the total runtime (multi-sample).	2013-02-21 10:14:11 -05:00
public	Improved allele trimming code in GATKVariantContextUtils	2013-02-21 12:01:43 -05:00
settings	Haplotype/Allele based optimizations for the HaplotypeCaller that knock off nearly 20% of the total runtime (multi-sample).	2013-02-21 10:14:11 -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