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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo e9c22b9aad Final updates to integration tests for BCF2 
-- Fully working version
-- Use -generateShadowBCF to write out foo.bcf as well as foo.vcf anywhere you use -o foo.vcf
-- Moved MedianUnitTest to its proper home in Utils
-- Added reportng to ivy and testng, so build/report/X/html/ is a nicely formatted output for Unit and Integration tests.  From this website it's easy to see md5 diffs, etc.  This is a vastly better way to manage unit and integration test output
 		2012-05-24 10:58:59 -04:00
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CNV GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
annotator GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
beagle Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
bqsr Removed old GATKReport code and moved the new stuff in its place. 2012-05-18 01:44:31 -04:00
coverage DoC now properly handles reference N bases + misc. additional cleanups 2012-02-25 11:32:50 -05:00
diagnostics Extensive refactoring of the GATKReports. This was a beast. 2012-05-18 01:11:26 -04:00
diffengine Has anyone else ever noticed that the DiffEngine outputs were always doubled for some reason? That no longer happens with the new reports. 2012-05-18 02:32:20 -04:00
fasta Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
filters GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
genotyper GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
indels GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
phasing GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
recalibration GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
validation GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
varianteval Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
variantrecalibration GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
variantutils Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
FlagStatIntegrationTest.java Adding integration test for Flag Stat 2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now. 2012-04-02 14:27:36 -04:00
PrintReadsIntegrationTest.java GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
PrintReadsUnitTest.java Better location for the downsampling of reads in PrintReads 2012-01-14 14:06:09 -05:00