baf3e33730
Allele refactoring checkpoint 2: all code finally compiles, AD and STR annotations are fixed, and most of the UG integration tests pass.
2012-07-26 23:27:11 -04:00
a694d1b5de
Merge branch 'master' into allelePadding
2012-07-26 01:53:14 -04:00
32516a2f60
Initial checkpoint commit of VariantContext/Allele refactoring. There were just too many problems associated with the different representation of alleles in VCF (padded) vs. VariantContext (unpadded). We are moving VC to use the VCF representation. No more reference base for indels in VC and no more trimming and padding of alleles. Even reverse trimming has been stopped (the theory being that writers of VCF now know what they are doing and often want the reverse padding if they put it there; this has been requested on GetSatisfaction). Code compiles but presumably pretty much all tests with indels with fail at this point.
2012-07-26 01:50:39 -04:00
1e8610b2c6
Merged bug fix from Stable into Unstable
2012-07-25 23:14:15 -04:00
8c418a15da
Sorting out HMS error handling (fingers crossed)
...
-- Check if a traversal error occurred in the last shard
-- Catch ExecutionException from the TreeReducer and throw as our HMS execption
-- ShardTraverser just throws the exception as formatted by the HMS, rather than wrapping it as a RuntimeException itself
-- EngineFeaturesIntegrationTests now uses public exampleFASTA (faster), and does 1000x iterations (slower)
2012-07-25 23:13:12 -04:00
5e9e1101a3
Merged bug fix from Stable into Unstable
2012-07-25 22:11:35 -04:00
9242f63a4d
On the way to really sorting out HMS error handling
...
-- Better error message when a traveral error occurs (a real bug)
-- EngineFeaturesIntegrationTest runs the multi-threaded error testing routines 50x times
-- A bit of cleanup in WalkerTest
2012-07-25 22:11:10 -04:00
5671992db3
RMDTrackBuilderUnitTest now uses private/testdata file to avoid filesystem race conditions
2012-07-25 22:05:04 -04:00
2949ecab40
Merged bug fix from Stable into Unstable
2012-07-25 21:41:09 -04:00
7eb3f54750
Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers.
2012-07-25 21:40:28 -04:00
2982b24c4b
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2012-07-25 20:36:53 -04:00
0a98a6aa8d
Adding extraDocs tag per Mauricio's request
2012-07-25 18:23:18 -04:00
6857b91aec
Merged bug fix from Stable into Unstable
2012-07-25 17:23:15 -04:00
fce5cb9f35
Few category changes
2012-07-25 17:23:02 -04:00
68193ecf2e
Merged bug fix from Stable into Unstable
2012-07-25 16:06:09 -04:00
05fa377a8e
Adding GATK categories to standard walkers. Will add to remaining walkers after the next successful release (so that I can see which walkers are public and still need it).
2012-07-25 16:05:47 -04:00
c85a557311
Merged bug fix from Stable into Unstable
2012-07-25 15:25:34 -04:00
d46cf47bd1
Updating Read Filter documentation
2012-07-25 15:05:47 -04:00
304c3e9802
Merged bug fix from Stable into Unstable
2012-07-25 14:12:00 -04:00
6a3bfa3811
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2012-07-25 14:11:11 -04:00
357e0b35af
Register GATK-full-only walkers and rethrow the missing walker error as a not supported in GATK lite error
2012-07-25 14:11:03 -04:00
1e4816e150
Merged bug fix from Stable into Unstable
2012-07-25 13:47:07 -04:00
5b74763096
Removed Categories.
...
We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything.
Tools can be hidden from GATKdocs with the @Hidden annotation
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-25 13:46:24 -04:00
a5721a8846
Context covariate optimizations were not suited for multiple threads, so I removed them (since that ended up being much, much easier than trying to make the covariates thread local). Added -nt 2 layer to BQSR integration tests to confirm that it now works with multiple threads.
2012-07-25 13:38:07 -04:00
e0c07f5567
Reverting old commits that made error handling better because ultimately they made things worse.
2012-07-25 12:37:59 -04:00
0285c1fe9e
Ensure that PrintReads has enough RAM
2012-07-25 10:52:16 -04:00
aef77e96d8
Combine BAMs using PrintReads
2012-07-25 10:52:16 -04:00
3df058a8f3
Test for processing many BAMs at once
2012-07-25 10:52:16 -04:00
f5f61d28b7
Merged bug fix from Stable into Unstable
2012-07-25 09:01:21 -04:00
66b409921a
Testfile for VF integration test
2012-07-25 09:00:55 -04:00
16947e93f2
Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR
...
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:39 -04:00
fcefa61bce
Remove reference dependence in BCF2Codec
...
-- Adding BCF2Codec to VCF.jar and associated unit tests
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:38 -04:00
19a257a5c1
Multiple bugfixes
...
-- VariantFiltration now properly sets passFilters in VC
-- BCF2 writer now properly decodes lazy BCF genotype data that it uses. Improper use generated a horrible subtle bug but the good news is that the extra checks I put in (unnecessarily a few days ago) caught the bug!
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:38 -04:00
3066894215
Bugfix for BCF2
...
-- Always decode genotypes block when writing out a BCF file. If the header changes (and we currently don't know this easily) then the dictionary keys used in the genotypes block may be invalid. Temporarily added a private static boolean that turns off writing of the blocks until Eric and his team rewrite the header.
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:38 -04:00
a99f3d6adf
Don't use old CC and TR commands. Not fixing for now, just want to see whether I can get this to pass first.
...
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
2012-07-25 08:56:38 -04:00
055792d99c
Merged bug fix from Stable into Unstable
2012-07-24 20:33:34 -04:00
61ee7983d4
Don't use old CC and TR commands. Not fixing for now, just want to see whether I can get this to pass first.
2012-07-24 12:26:39 -04:00
eb55061fd0
a) Document BEAGLE codec, b) Bug fix: inbreeding coefficient shouldn't be computed for non-diploid organisms in current implementaiton
2012-07-24 12:16:15 -04:00
c011837147
Merge remote-tracking branch 'unstable/master'
2012-07-24 11:15:31 -04:00
348e86159e
Moving doclets to public
2012-07-23 23:52:14 -04:00
0cca75a290
Updated IWWW_DIR and WWW_DIR paths, and switch 'mv' to 'rsync' as requested by carneiro.
2012-07-23 23:29:00 -04:00
5cd98a36b9
Making ForumAPIUtils public
2012-07-23 17:44:24 -04:00
3d92f041f3
forgot to delete the merging line
2012-07-23 17:35:07 -04:00
f3c504769b
Added the ability to update the Forum
...
GATKDocs looks for a key on gsa4, and updates the forum with new walker if it exists.
More changes were made to the GATKDocs. Works nicely with bootstrap on and offline.
Cleaned up the code as well
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-07-23 17:17:33 -04:00
46ca49b63d
Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.
...
Archived AnalyzeCovariates scripts and removed references in build packages / GATK extensions.
2012-07-23 16:32:31 -04:00
a9ad9b3880
Inserted final paths for binaries.
2012-07-23 14:29:10 -04:00
41df9bd2a2
Moving BQSR plotting script to public so that it can be used with the substiution-model-only version.
2012-07-23 11:46:07 -04:00
2a14bbe4f0
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-23 11:28:26 -04:00
10d143c35c
Adding error model header names in the BQSR recal plot. Making the downsampling of points look a little nicer.
2012-07-23 11:28:17 -04:00
675ccab2fa
Renaming BQSR to BaseRecalibrator
2012-07-23 10:17:17 -04:00
Eric Banks
Mark DePristo
Mauricio Carneiro
Roger Zurawicki
Joel Thibault
Guillermo del Angel
Khalid Shakir
Ryan Poplin