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
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R	Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.	2011-07-02 10:39:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00
packages	Removed TileCovariate as a dependency for AnalyzeCovariates.jar	2011-07-11 12:10:11 -04:00
perl	Moving these supported perl scripts to public	2011-07-01 17:26:25 -04:00
scala	Merged bug fix from Stable into Unstable	2011-07-17 18:10:18 -04:00
testdata	First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure.	2011-07-04 16:11:42 -04:00