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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
History
Christopher Hartl 4a08e8ca6e Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .) 
This is somewhat of an arbitrary decision, and is negotiable. I could see treating

GT:PL   ./.:.

differently from

GT:PL   .:0,3,6

but am not sure the worth of doing so.
 		2012-01-23 08:25:34 -05:00
..
CNV Updating md5 because the file changed 2011-09-23 07:33:20 -04:00
annotator updating TDT integration test 2012-01-18 09:52:50 -05:00
beagle Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .) 2012-01-23 08:25:34 -05:00
coverage Patching special case in the adaptor clipping 2012-01-11 17:47:44 -05:00
diffengine Right aligning GATKReport numeric columns and updated MD5s in tests. 2011-12-05 23:22:15 -05:00
fasta Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
filters Again, fixing the add call when we really mean replace 2011-11-21 19:15:56 -05:00
genotyper Annotate with FS even for filtered sites 2012-01-18 22:04:51 -05:00
indels Rename *PerformanceTest test classes to *LargeScaleTest 2011-12-22 10:38:49 -05:00
phasing Merge with master 2011-11-19 09:56:06 -05:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
recalibration Patching special case in the adaptor clipping 2012-01-11 17:47:44 -05:00
validation Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative. 2011-10-27 23:55:11 -04:00
varianteval Bug fix for VariantSummary 2012-01-05 21:51:06 -05:00
variantrecalibration Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts. 2011-09-12 12:17:43 -04:00
variantutils Bug fix: if there are multiple records at a given position, it turns out that SelectVariants would drop all variants that follow after one that fails filters (instead of dropping just the failing one). Added an integration test to cover this case. 2011-12-19 10:04:33 -05:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java Updating MD5s for updated BAM with read groups 2011-10-06 12:15:48 -07:00
PileupWalkerIntegrationTest.java Updated integration tests for the new adaptor clipping fix. 2011-12-30 18:47:14 -05:00
PrintReadsIntegrationTest.java
…
PrintReadsUnitTest.java Better location for the downsampling of reads in PrintReads 2012-01-14 14:06:09 -05:00