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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Khalid Shakir 5dcac7b064 GATKReport v0.2: 
- Floating point column widths are measured correctly
- Using fixed width columns instead of white space separated which allows spaces embedded in cell values
- Legacy support for parsing white space separated v0.1 tables where the columns may not be fixed width
- Enforcing that table descriptions do not contain newlines so that tables can be parsed correctly
Replaced GATKReportTableParser with existing functionality in GATKReport
 		2011-08-03 00:24:47 -04:00
..
annotator Removing the Genomic Annotator and its supporting classes 2011-07-25 15:10:25 -04:00
beagle 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
coverage Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
diffengine GATKReport v0.2: 2011-08-03 00:24:47 -04:00
fasta Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
filters 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
genotyper The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD 2011-08-02 10:14:21 -04:00
indels Adding back temporarily removed integration test now that the file permissions have been fixed. 2011-08-02 12:39:11 -04:00
phasing Updated MD5 for PhaseByTransmissionIntegrationTest 2011-07-26 17:52:25 -04:00
qc Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
recalibration Removing --DBSNP syntax from BQSR integration tests 2011-08-02 15:34:38 -04:00
validation When using the BWA bindings, you have to explicitly call close() to get the 2011-07-21 12:13:29 -04:00
varianteval GATKReport v0.2: 2011-08-03 00:24:47 -04:00
variantrecalibration Walker test system refactoring. All MD5DB related functions are now in MD5DB.java. 2011-07-18 10:46:01 -04:00
variantutils GATKReport v0.2: 2011-08-03 00:24:47 -04:00
BAQIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ClipReadsWalkersIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PileupWalkerIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PrintReadsIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PrintReadsWalkerUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00