gatk3的最后一个经典版本3.8

Ryan Poplin 1f254d29df Don't set the empirical quality when reading in the recal table because then we won't be using the new quality estimates for the prior since the value is cached.		2013-01-28 22:16:43 -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	Don't set the empirical quality when reading in the recal table because then we won't be using the new quality estimates for the prior since the value is cached.	2013-01-28 22:16:43 -05:00
public	The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior.	2013-01-28 15:56:33 -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