5f82ffd5d8
Adding LowQual filter to the output of the HaplotypeCaller.
2012-08-10 11:25:14 -04:00
67d4148b32
Fixing but reported by Thomas in the forum where reads were soft-clipped beyond the limits of the contig and ReduceReads was failing with a NoSuchElement exception. Now we hard clip anything that goes beyond the boundaries of the contig.
2012-08-09 15:58:18 -04:00
c6132ebe26
Fixed divide by zero bug when downsampler goes over regions where reads are all filtered out. Added Guillermo's bug report as an integration test
2012-08-09 13:02:11 -04:00
78c1556186
Fixing ReduceReads downsampling bug -- downsampled reads were not being excluded from the read window, causing them to trail back and get caught by the sliding window exception
2012-08-08 15:49:31 -04:00
f40d0a0a28
Updating VQSR to work with the MNP and symbolic variants that are coming out of the HaplotypeCaller. Integration tests change because of the MNPs in dbSNP.
2012-08-03 10:44:36 -04:00
6f7a236cfc
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2012-08-02 11:41:20 -04:00
cb8bc18aeb
Fix for error in HaplotypeCaller. HC has a UG argument collection for the UG engine but some of those arguments aren't appropriate to set.
2012-08-02 11:41:06 -04:00
0381fd7c83
Hmm, I thought I used the right md5s last time. Let's try again.
2012-08-02 11:25:10 -04:00
fabca66d09
Another fix to VQSR docs
2012-08-01 14:52:49 -04:00
4093909a56
Updating VQSR docs. Removing references to old best practices pages.
2012-08-01 14:30:24 -04:00
22bf052828
Fixing BQSR GATK docs
2012-08-01 13:17:16 -04:00
84cd23f891
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2012-08-01 10:55:37 -04:00
01265f78e6
Add sanity check and possible bug fix for forum user: if haplotypes cannot be created from given alleles when genotyping indels (e.g. too close to contig boundary, etc.) in pool mode, empty allele list, signifying site can't be genotyped
2012-08-01 10:50:00 -04:00
05bf6e3726
Updating md5s in pipeline tests so that they finally pass
2012-08-01 10:27:00 -04:00
56f8afab97
Requested by Geraldine: adding a utility to register deprecated walkers (and the major version of the first release since they were removed) so that the User Error printed out for e.g. CountCovariates now states: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0.
2012-08-01 09:50:00 -04:00
7cf4b63d76
Disabling indel quals in BaseRecalibrator as it should be, not PrintReads.
2012-08-01 09:23:04 -04:00
79195b97a3
Adding categories for the remaining uncategorized walkers
2012-07-30 11:35:08 -04:00
4f741b4cd7
Smoothing in the BQSR bins should be one error observation and one non-error observation.
2012-07-26 13:59:02 -04:00
8c418a15da
Sorting out HMS error handling (fingers crossed)
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-- 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
9242f63a4d
On the way to really sorting out HMS error handling
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-- 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
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
fce5cb9f35
Few category changes
2012-07-25 17:23:02 -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
d46cf47bd1
Updating Read Filter documentation
2012-07-25 15:05:47 -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
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
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
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-- 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
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-- 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
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
Ryan Poplin
Mauricio Carneiro
Eric Banks
Guillermo del Angel
Mark DePristo
Roger Zurawicki
Khalid Shakir