..
CNV
BCF2 with support symbolic alleles
2012-06-30 11:22:48 -04:00
annotator
QD is now divided by the average length of the alternate allele (weighted by the allele count). The average length is stored in a related annotation, "AAL", which can be used to re-compute the "old" QD by simple multiplication. Integration tests *should* all pass.
2013-01-02 14:41:29 -05:00
beagle
Fixing remaining integration test errors. Adding missing ex2.bcf
2012-06-30 16:23:11 -04:00
bqsr
Cleanup and unit tests for EventType and ReadRecalibrationInfo in BQSR
2013-01-04 11:39:25 -05:00
coverage
Fix bugs as reported on the forum: BED needs to be explicitly set as the default output format and the output didn't actually adhere to the BED spec.
2012-11-08 15:07:47 -05:00
diagnostics
Fixing remaining integration test errors. Adding missing ex2.bcf
2012-06-30 16:23:11 -04:00
diffengine
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
2012-12-19 10:25:22 -05:00
fasta
Several more walkers have been brought up to use the new Allele representation.
2012-07-27 02:14:25 -04:00
filters
Fixing problem reported on forum for VF: DP couldn't be filtered from the FORMAT field, only from the INFO field. Fixed and added integration test.
2012-10-26 00:57:40 -04:00
genotyper
ArtificialReadPileupTestProvider now creates GATKSamRecords with good header values
2012-12-24 13:35:57 -05:00
indels
Allow large-scale tests 5 hours each to run
2012-11-01 17:48:58 -04:00
phasing
Fix for PBT bug reported on the forum: the AD is actually output correctly now (rather than with 'null' or some gibberish memory pointer).
2012-12-13 23:28:30 +00:00
qc
First version of VariantContextBuilder
2011-11-18 11:06:15 -05:00
validation
Allele refactoring checkpoint #3 : all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this.
2012-07-27 15:48:40 -04:00
varianteval
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
2012-12-19 10:25:22 -05:00
variantrecalibration
Fixing md5s to reflect the new HapMap file
2012-10-30 14:27:10 -04:00
variantutils
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
2012-12-19 10:25:22 -05:00
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
some changes.
2012-12-14 17:21:32 -05:00
PrintReadsIntegrationTest.java
ReadShard are no longer allowed to span multiple contigs
2012-08-30 10:15:11 -04:00
PrintReadsLargeScaleTest.java
PrintReads large-scale test to protect against another major low-level performance issue
2012-12-05 21:36:27 -05:00
PrintReadsUnitTest.java
Removed the "Walker" suffix from all walkers that had it.
2012-07-20 17:27:11 -04:00
810e2da1d4