gatk3的最后一个经典版本3.8

Mauricio Carneiro fdd16dc6f9 DiagnoseTargets refactor ... A plugin enabled implementation of DiagnoseTargets Summarized Changes: ------------------- * move argument collection into Thresholder object * make thresholder object private member of all statistics classes * rework the logic of the mate pairing thresholds * update unit and integration tests to reflect the new behavior * Implements Locus Statistic plugins * Extend Locus Statistic plugins to determine sample status * Export all common plugin functionality into utility class * Update tests accordingly [fixes #48465557]		2013-04-22 23:53:10 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	DiagnoseTargets refactor	2013-04-22 23:53:10 -04:00
public	Minor: bump up the amount of cached log10 data in MathUtils so that Monkol can actually call 50K samples.	2013-04-19 08:39:08 -04:00
settings	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Disable Contracts for Java for tests	2013-04-04 11:56:17 -04:00
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