| .. |
|
CNV
|
BCF2 with support symbolic alleles
|
2012-06-30 11:22:48 -04:00 |
|
annotator
|
FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing
|
2012-07-18 16:07:47 -04:00 |
|
beagle
|
Fixing remaining integration test errors. Adding missing ex2.bcf
|
2012-06-30 16:23:11 -04:00 |
|
bqsr
|
Reverting move of BQSR tests to public, as per DR's email
|
2012-07-19 10:02:05 -04:00 |
|
coverage
|
DoC now properly handles reference N bases + misc. additional cleanups
|
2012-02-25 11:32:50 -05:00 |
|
diagnostics
|
Fixing remaining integration test errors. Adding missing ex2.bcf
|
2012-06-30 16:23:11 -04:00 |
|
diffengine
|
Cleanup of VCF header lines and constants, BCF2 bugfixes
|
2012-06-21 15:16:31 -04:00 |
|
fasta
|
Removing the legacy -L "interval1;interval2" syntax
|
2011-11-21 13:18:53 -05:00 |
|
filters
|
Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR
|
2012-07-25 08:56:39 -04:00 |
|
genotyper
|
Fix md5's broken by recent changes to FisherStrand calculation
|
2012-07-21 14:41:38 -04:00 |
|
indels
|
Cleanup of VCF header lines and constants, BCF2 bugfixes
|
2012-06-21 15:16:31 -04:00 |
|
phasing
|
- Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE
|
2012-07-17 15:21:10 -04:00 |
|
qc
|
First version of VariantContextBuilder
|
2011-11-18 11:06:15 -05:00 |
|
validation
|
Cleanup of VCF header lines and constants, BCF2 bugfixes
|
2012-06-21 15:16:31 -04:00 |
|
varianteval
|
Removed the "Walker" suffix from all walkers that had it.
|
2012-07-20 17:27:11 -04:00 |
|
variantrecalibration
|
In ApplyRecalibration marking filter as PASS instead of '.' when the site passes by calling .passFilters().
|
2012-07-13 15:40:56 -04:00 |
|
variantutils
|
Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants
|
2012-07-10 13:59:00 -04:00 |
|
BAQIntegrationTest.java
|
merge master
|
2011-10-25 16:08:39 -04:00 |
|
ClipReadsWalkersIntegrationTest.java
|
Cleanup of VCF header lines and constants, BCF2 bugfixes
|
2012-06-21 15:16:31 -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
|
Cleanup of VCF header lines and constants, BCF2 bugfixes
|
2012-06-21 15:16:31 -04:00 |
|
PrintReadsUnitTest.java
|
Removed the "Walker" suffix from all walkers that had it.
|
2012-07-20 17:27:11 -04:00 |
16947e93f2