gatk3的最后一个经典版本3.8

Guillermo del Angel 5995f01a01 Big intermediate commit (mostly so that I don't have to go again through merge/rebase hell) in expanding BQSR capabilities. Far from done yet: ... a) Add option to stratify CalibrateGenotypeLikelihoods by repeat - will add integration test in next push. b) Simulator to produce BAM files with given error profile - for now only given SNP/indel error rate can be given. A bad context can be specified and if such context is present then error rate is increased to given value. c) Rewrote RepeatLength covariate to do the right thing - not fully working yet, work in progress. d) Additional experimental covariates to log repeat unit and combined repeat unit+length. Needs code refactoring/testing		2013-01-28 19:55:46 -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	Big intermediate commit (mostly so that I don't have to go again through merge/rebase hell) in expanding BQSR capabilities. Far from done yet:	2013-01-28 19:55:46 -05:00
public	Big intermediate commit (mostly so that I don't have to go again through merge/rebase hell) in expanding BQSR capabilities. Far from done yet:	2013-01-28 19:55:46 -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	Remove the ability to package GATK/Queue Lite from the build system	2013-01-28 02:42:37 -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