gatk3的最后一个经典版本3.8

Eric Banks 9c0207f8ef Fixing BQSR/BAQ bug: ... If a read had an existing BAQ tag, was clipped by our engine, and couldn't have the BAQ recalculated (for whatever reason), then we would fail in the BQSR because we would default to using the old tag (which no longer matched the length of the read bases). The right thing to do here is to remove the old BAQ tag when RECALCULATE and ADD_TAG are the BAQ modes used but BAQ cannot be recalculated. Added a unit test to ensure that the tags are removed in such a case.		2013-01-31 11:03:17 -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	Merge branch 'master' of github.com:broadinstitute/gsa-unstable	2013-01-31 10:12:26 -05:00
public	Fixing BQSR/BAQ bug:	2013-01-31 11:03:17 -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	Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs	2013-01-30 16:42:23 -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	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00