| .. |
|
CNV
|
Updating md5 because the file changed
|
2011-09-23 07:33:20 -04:00 |
|
activeregionqc
|
There are now three triggering options in the HaplotypeCaller. The default (mismatches, insertions, deletions, high quality soft clips), an external alleles file (from the UG for example), or extended triggers which include low quality soft clips, bad mates and unmapped mates. Added better algorithm for band pass filtering an ActivityProfile and breaking them apart when they get too big. Greatly increased the specificity of the caller by battening down the hatches on things like base quality and mapping quality thresholds for both the assembler and the likelihood function.
|
2012-04-10 14:48:23 -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
|
Implementation of the new BQSR plotting infrastructure
|
2012-04-17 19:23:55 -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
|
Khalid pressured me into adding an integration test that makes sure we don't fail on reads with adjacent I and D events.
|
2012-04-17 21:21:29 -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
|
Update VE IT to reflect new fields and bugfixes
|
2012-04-13 17:00:37 -04:00 |
|
variantrecalibration
|
Final tweaks. Added an integration test to cover the case of SNPs and indels that start at the same position.
|
2012-04-17 23:54:10 -04:00 |
|
variantutils
|
Final update for VE. VCFStreaming wasn't yet updated
|
2012-03-30 21:52:01 -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 |
4448a3ea76