gatk3的最后一个经典版本3.8

Eric Banks e7c35a907f Fixes to BQSR for the --maximum_cycle_value argument. ... - It's now written into the recal report so that it can be used in the PrintReads step. - Note that we also now write the --deletions_default_quality value which accidentally wasn't being written before! - Added tests to make sure that the value of the --maximum_cycle_value is being used properly by PR with -BQSR. (This is my last non-branch commit; all future pushes will follow new GATK practices)		2013-02-05 17:38:03 -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	Fixes to BQSR for the --maximum_cycle_value argument.	2013-02-05 17:38:03 -05:00
public	Fixing license on Yossi's file	2013-02-05 11:14:43 -05:00
settings	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -05:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Move AWS keys to a resources subdirectory within the phonehome package	2013-01-31 11:56:34 -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