gatk3的最后一个经典版本3.8

Mark DePristo c97a361b5d Added realistic BandPassFilterUnitTest that ensures quality results for 1000G phase I VCF and NA12878 VCF ... -- Helped ID more bugs in the ActivityProfile, necessitating a new algorithm for popping off active regions. This new algorithm requires that at least maxRegionSize + prob. propagation distance states have been examined. This ensures that the incremental results are the same as you get reading in an entire profile and running getRegions on the full profile -- TODO is to remove incremental search start algorithm, as this is no longer necessary, and nicely eliminates a state variable I was always uncomfortable with		2013-01-27 14:10:08 -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	HaplotypeCaller Optimization: return a inactive (p = 0.0) activity if the context has no bases in the pileup	2013-01-27 14:10:06 -05:00
public	Added realistic BandPassFilterUnitTest that ensures quality results for 1000G phase I VCF and NA12878 VCF	2013-01-27 14:10:08 -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