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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baq	Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.	2011-06-30 14:59:58 -04:00
bed	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
codecs	Tests needed to be updated to reflect the code reorg of tribble.	2011-07-16 09:22:34 -04:00
collections	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
fasta	Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache	2011-07-01 16:04:30 -04:00
genotype	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00
interval	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
pileup	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
report	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
sam	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
text	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
threading	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
variantcontext	This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.	2011-07-12 14:11:53 -04:00
BaseUtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenomeLocParserUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenomeLocSortedSetUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenomeLocUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
MWUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
MathUtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PathUtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ReadUtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ReservoirDownsamplerUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
SimpleTimerUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
UtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00