gatk3的最后一个经典版本3.8

Mauricio Carneiro ef4cc742e5 Fixing the licensing scripts ... - Fixed shell glob limitation that was failing license updates on big commits - Hook will now force user to re-commit after updating the licenses (pre-commit hook can't update and commit in the same process) - Moved all scripts to bash/zsh - Separated the license utilities in a separate python module to avoid copying code GSATDG-28 #resolve		2013-01-26 13:42:49 -05:00
licensing	Refrain from pushing symlinks into the repo... not all filesystems treat it correctly	2013-01-22 15:18:19 -07:00
protected/java	In cases where one uses VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE we used to verify that the samples names are unique in VariantContextUtils.simpleMerge for each VCs. It couse to a bug that was reported on the forum (when a VCs had 2 VC from the same sample).	2013-01-25 15:49:51 -05:00
public	Making metrics a required parameter in MarkDuplicates	2013-01-25 17:49:49 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
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