..
CNV
Updating md5 because the file changed
2011-09-23 07:33:20 -04:00
activeregionqc
Fixing a bug when breaking up active regions where the resulting regions would overlap by one base. Adding quality score manipulation from the UG into the haplotype caller (qual capped by mapping quality, min qual threshold).
2012-04-20 14:02:55 -04:00
annotator
Updating integration tests now that standard annotations support multiple alleles
2012-02-27 11:32:26 -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
bqsr
BQSR triage and test routines
2012-04-23 11:23:00 -04:00
coverage
DoC now properly handles reference N bases + misc. additional cleanups
2012-02-25 11:32:50 -05:00
diagnostics
GATKReport v1.0
2012-03-12 23:09:19 -04:00
diffengine
Fixing MD5's (new GATKReport header was missing from old md5's)
2012-03-19 15:28:45 -04:00
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
If we are subsetting alleles in the UG (either because there were too many or because some were not polymorphic), then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). Thanks to Ryan for reporting this. Only one of the integration tests had even partially covered this case, so I added one that did.
2012-04-20 17:00:05 -04:00
indels
Removing dependence on extended events from the RealignerTargetCreator. Did some minor refactoring while I was in there.
2012-03-30 10:33:30 -04:00
phasing
Added respectPhaseInInput flag to RBP and integration tests
2012-03-22 17:40:21 -04:00
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
Added integration test for ValidationSiteSelector, correct MD5's
2012-03-26 16:39:55 -04:00
varianteval
AC strat now checks if evals will be merged before throwing an error on multiple eval files.
2012-04-19 16:08:55 -04:00
variantrecalibration
Removed experimental feature (aka hack) that was meant for 1000G consensus but remained in VQSR data manager - QD was being scaled by indel length. There's no evidence any more that QD is length-dependent, neither in CEU trio data nor in latest 1000G P2 calls
2012-04-20 10:58:34 -04:00
variantutils
When running SelectVariants with the excludeNonVariants option, remove alleles from the ALT field that are no longer polymorphic.
2012-04-20 14:30:04 -04:00
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
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
Reorganized the codebase beneath top-level public and private directories,
2011-06-28 06:55:19 -04:00
PrintReadsUnitTest.java
Better location for the downsampling of reads in PrintReads
2012-01-14 14:06:09 -05:00
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