gatk-3.8

Author	SHA1	Message	Date
Mark DePristo	2ebdff074c	Update MD5s for SOLiD recalibration -- MD5 db had spelling error; fixed -- Bug in AlignmentUtils resulted in some bases not being color space corrected. The integration test caught the change, and it's clear that the new version is correct, as the prev. version was not considering the last the N qualities for reads with a ND operation.	2011-10-13 18:01:51 -04:00
Mark DePristo	f6a5e0e36a	Go for global integrationtest path first, if possible.	2011-07-26 17:35:30 -04:00
Mark DePristo	3afcb3415d	Max of 1000 records will be loaded and compared to avoid heap size problem.	2011-07-25 14:58:31 -04:00
Mark DePristo	d6e2e89f99	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java. System has the concept of a local and a global MD5 db. The local one is like it operated previously. The global one lives in /humgen/gsa-hpprojects/GATK/data/integrationtests. If the system can find this directory then MD5s will also be read / written to this location. This means that gsabamboo will print differences as appropriate. And all users will in effect have access to a complete history of MD5 file results. A few minor code reshuffles changed VariantRecalibration and VCFHeader test files.	2011-07-18 10:46:01 -04:00