gatk3的最后一个经典版本3.8

Mark DePristo 4095a9ef32 Bugfixes for AssessNA12878 ... -- Refactor initialization routine into BadSitesWriter. This now adds the GQ and DP genotype header lines which are necessarily if the input VCF doesn't have proper headers -- GATKVariantContextUtils subset to biallelics now tolerates samples with bad GL values for multi-allelics, where it just removes the PLs and issues a warning.		2013-02-28 10:35:06 -05:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Merge pull request #73 from broadinstitute/eb_remove_nested_hashmap_GSA-732	2013-02-28 05:19:56 -08:00
public	Bugfixes for AssessNA12878	2013-02-28 10:35:06 -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	Updating TestNG to the latest version	2013-02-22 09:40:23 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00