Eric Banks 15ae906f32 Once I was playing with integration tests it was simple to fix the ones I left broken from earlier today.		2012-06-18 21:54:58 -04:00
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CNV	…
annotator	Optimizations for VCF and BCF2	2012-06-14 16:42:39 -04:00
beagle	Optimizations for VCF and BCF2	2012-06-14 16:42:39 -04:00
bqsr	Ryan confirmed that we don't need separate arguments to control the context size for insertions and deletions, which allows us to cut down the expensive context calculations.	2012-06-15 09:28:56 -04:00
coverage	…
diagnostics	…
diffengine	…
fasta	…
filters	…
genotyper	Emit the MLE AC and AF in the INFO field of the UG output	2012-06-18 12:19:36 -04:00
indels	…
phasing	…
qc	…
recalibration	…
validation	…
varianteval	If present, VE's AlleleCount stratification uses the MLE AC by default (and otherwise drops down to use the greedy AC). Added integration test to cover it.	2012-06-18 13:36:14 -04:00
variantrecalibration	…
variantutils	Once I was playing with integration tests it was simple to fix the ones I left broken from earlier today.	2012-06-18 21:54:58 -04:00
BAQIntegrationTest.java	…
ClipReadsWalkersIntegrationTest.java	…
FlagStatIntegrationTest.java	…
PileupWalkerIntegrationTest.java	…
PrintReadsIntegrationTest.java	…
PrintReadsUnitTest.java	…