bd29236684
Merge branch 'master' into diffengine
2011-07-08 14:08:17 -04:00
2a4b3ae4a2
Cleaning up / removing most of the monkeying around with annotation values that happens in VariantDataManager
2011-07-08 12:48:33 -04:00
8add2a3866
Merge branch 'master' into diffengine
2011-07-08 09:15:54 -04:00
cc143493e3
Merged bug fix from Stable into Unstable
2011-07-07 23:01:24 -04:00
4cfe0dd857
Test for bad alleles so that we don't generate IndexOutOfBoundsExceptions
2011-07-07 23:01:03 -04:00
3d4f0e9dd7
Now supports the case where you have multiple AC values in the info field.
2011-07-07 17:21:15 -04:00
212e9a1a0c
Fixing unstable build after stable commit
2011-07-07 15:18:57 -04:00
11d9a0473a
Merged bug fix from Stable into Unstable
2011-07-07 15:03:58 -04:00
50111db2b7
Fixing non-determinism in single-threaded VQSR by moving references to cern.Normal over to the static random generator available in GenomeAnalysisEngine
2011-07-07 15:02:48 -04:00
ccf34f7e45
(1) Added very useful helper class TestDataProvider to BaseTest that making creating data providers for TestNG far easier
...
(2) DiffEngine now officially working with with summaries. Extensive UnitTests all around!
2011-07-06 21:57:22 -04:00
52f6f9fdcc
Merged bug fix from Stable into Unstable
2011-07-06 16:05:48 -04:00
54121eb082
Catch malformed bams that cause the writer to run in infinite loops
2011-07-06 16:05:08 -04:00
76a01a7453
Merged bug fix from Stable into Unstable
2011-07-06 12:53:09 -04:00
14fee4ccbd
Patch from Bob to deal with symbolic alleles: these weren't getting padded but they should be.
2011-07-06 12:51:44 -04:00
bdef233d4d
Merged bug fix from Stable into Unstable
2011-07-06 10:05:02 -04:00
e8ed6b7f0f
Adding more comments to main VQSR walker. Fixing copyright lines. Bug fix for default paths to now point to public/R/ instead of R/ Bug fix in VQSR for the path to the R scripts not ending in a slash.
2011-07-06 10:01:14 -04:00
8e8b901d12
Merged bug fix from Stable into Unstable
...
Merge branch 'master' into unstable
2011-07-06 09:57:55 -04:00
81a4d18468
Mark several indel-related arguments as @Hidden
2011-07-06 09:56:38 -04:00
fb315b5f8c
Merge branch 'incoming'
2011-07-02 18:10:48 -04:00
41d46059e7
fixing bad format statement
2011-07-02 18:09:17 -04:00
3804afeb8a
Merge branch 'incoming'
2011-07-02 17:55:39 -04:00
781c0c33a4
Use the worst X% of calls in addition to the bad training sites list. Don't include the already added calls in the calculation of X%
2011-07-02 17:55:10 -04:00
6b8af6afd8
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 17:15:56 -04:00
fdc2ebb321
Adding ability to specify in VQSR a list of bad sites to use when training the negative model. Just add bad=true to the list of rod tags for your bad sites track.
2011-07-02 17:15:13 -04:00
09af6bbc6c
Ugh - backed out experimental code not for public consumption unintendedly committed
2011-07-02 16:58:57 -04:00
c6c0dba040
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 16:45:34 -04:00
4532a84314
Merged bug fix from Stable into Unstable
2011-07-02 10:48:55 -04:00
5faf40b79d
Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.
2011-07-02 10:39:53 -04:00
17ff5bb094
Variant records coming out of the VQSR are now annotated with which input annotation was most divergent from the Gaussian mixture model. This gives a general sense for why each variant was removed from the callset.
2011-07-02 09:55:35 -04:00
c65e52f88a
Merged bug fix from Stable into Unstable
2011-07-01 20:50:56 -04:00
b6bc64a0c8
Cleanup of the utils.broad package.
...
Using Picard IoUtils on sample names.
2011-07-01 20:47:03 -04:00
0c9105ca22
Minor fix of description
2011-07-01 18:07:35 -04:00
d647ea4fdc
Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache
...
non-static to avoid problems when multiple references are used within the same
thread (eg., during integration tests). This should kill the intermittent
IndelRealignerIntegrationTest failures.
2011-07-01 16:04:30 -04:00
761347b8d5
The VariantContext utility method used by SelectVariants wasn't checking the filter status (unfiltered vs. passing filters) and always returned a VC that was passing filters. This is fixed and the md5 from the VCF Streaming test has been re-updated.
2011-06-30 15:26:09 -04:00
867056af51
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:03:18 -04:00
defa3cfe85
Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.
2011-06-30 14:59:58 -04:00
2cb1376ed0
VCFStreaming was failing integration tests because now select variants outputs the samples in alphabetical order, instead of random as before. Fixed the MD5.
2011-06-30 14:55:39 -04:00
804d5f22d5
Reverting previous change, as promised.
2011-06-30 13:18:30 -04:00
9e234cf5d6
This is a temporary commit for Picard. It will absolutely break integration tests, but I'm going to revert it in 1 minute. Because we don't want them in unstable, I need to push this into stable.
2011-06-30 13:17:14 -04:00
352c38fc0b
Updated to reflect dbsnp conversion fix
2011-06-30 11:55:56 -04:00
331b47afbd
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-30 08:29:11 -04:00
f18fffd625
Fixing broken paths to the testdata directory throughout the codebase.
2011-06-29 17:36:47 -04:00
2b88033ef4
Enable considering 454 reads, just lower GOP by 15
2011-06-29 16:12:55 -04:00
dc4f63a1a8
a) consensus goes to week queue
...
b) New experimental TechnologyComposition annotation
c) SelectVariants fixes
2011-06-29 16:00:23 -04:00
70ba851478
Might as well check for the illegal state and throw an exception
2011-06-29 15:59:10 -04:00
1f19afe1d9
Fixed bug in the IndelRealigner: now that variants are correctly typed in VariantContext, it is possible that a variant can be an indel but neither an insertion or a deletion; added a isComplexIndel() method and now we check for such an event in the realigner (we don't use them to generate alternate consenses). Also, added a isMNP() method while I was there so that it would be consistent with other variant types.
2011-06-29 15:54:09 -04:00
e91ae6b265
AF matching when selecting random variants
2011-06-29 15:00:26 -04:00
33c67a139c
Wrong package; this should have been moved when VC got moved in from Tribble
2011-06-29 14:56:02 -04:00
dee10140dd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 13:58:04 -04:00
8586c86bc4
My commit from last week to fix the old dbsnp rod conversion only worked for locus traversals. Updated now to work for all traversals.
2011-06-29 13:56:37 -04:00
Mark DePristo
Ryan Poplin
Eric Banks
Guillermo del Angel
Khalid Shakir
David Roazen
Mauricio Carneiro