gatk3的最后一个经典版本3.8

Chris Hartl 327169b283 Refactor the method that identifies the site overlap type into the type enum class (so it can be used elsewhere potentially). ... Completed todo item: for sites like (eval) 20 12345 A C 20 12345 A AC (comp) 20 12345 A C 20 12345 A ACCC the records will be matched by the presence of a non-empty intersection of alleles. Any leftover records are then paired with an empty variant context (as though the call was unique). This has one somewhat counterintuitive feature, which is that normally (eval) 20 12345 A AC (comp) 20 12345 A ACCC would be classified as 'ALLELES_DO_NOT_MATCH' (and not counted in genotype tables), in the presence of the SNP, they're counted as EVAL_ONLY and TRUTH_ONLY respectively. + integration test		2013-01-15 12:13:45 -05:00
licensing	Cleaning CRLF terminations in the licenses	2013-01-10 17:06:29 -05:00
protected/java	Refactor the method that identifies the site overlap type into the type enum class (so it can be used elsewhere potentially).	2013-01-15 12:13:45 -05:00
public	Backporting LIBSPerformance improvements to original commit	2013-01-13 09:53:10 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Updating Queue maven version to 0.0.2	2013-01-10 13:46:49 -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	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00