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.
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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
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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
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-- 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.
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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
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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.
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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
2e486d83e2
Updating HaplotypeCaller docs and expanding integration tests.
2012-07-23 10:05:42 -04:00
cd4b0dda71
Protect against the context covariate or any other covariate blowing up the recalibration report PDF file because of having too many possible values.
2012-07-22 19:20:19 -04:00
35415a523d
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-22 16:54:39 -04:00
d38f3a071f
fixing typo in comments
2012-07-22 16:54:19 -04:00
39f45127f3
Fix md5's broken by recent changes to FisherStrand calculation
2012-07-21 14:41:38 -04:00
df965d4a5a
Fixing BQSR integration test
2012-07-21 11:11:45 -04:00
d7bffb0024
Final final final version of the license.
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Please make sure to use this one on the new webpage
2012-07-20 18:00:02 -04:00
65f4b67b86
Fixing walker unit test with the new naming convention
2012-07-20 17:50:29 -04:00
921eaad33f
Generalized the default platform parameter in BQSRv2
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Parameter wasn't working outside of the BQSR walker. It now takes the information on the recalibration report in other tools (PrintReads for example) and treats all reads as coming from the defined default platform.
2012-07-20 17:29:13 -04:00
5dc2143142
Removed support for walkers ending with "Walker" from the engine.
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If your walker has "Walker" in the name, you will have to use "Walker" on the -T to access it.
2012-07-20 17:27:11 -04:00
d446d34227
GATK Error messages now point to the new website instead of GetSatisfaction.
2012-07-20 17:27:11 -04:00
116885a450
Removed the "Walker" suffix from all walkers that had it.
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* Did not touch archived walkers... those can be named whatever.
* Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...)
* Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
2012-07-20 17:27:11 -04:00
dea049553a
Adding missing testdata file
2012-07-20 09:19:28 -04:00
3ee46cced2
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-19 21:25:40 -04:00
af383c30b5
Ensure that the gene summary has a header line
2012-07-19 21:24:04 -04:00
2ca5fc62a2
Support for MISSING BCF2 type
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-- Heng wants to use 0x0? to represent any missing type value, which in our implementation was invalid. Updated our codebase to support this construct. Heng said he'll update the BCF2 quick reference.
-- Enabled integration test reading Heng's ex2.bcf file
-- GATK now only warns in the case where the END info field isn't the same (or +1 due to padding) as the getEnd() function as determined by the GATK. Turns out there's a single record in the 1000G SV call set that doesn't have the right length
-- VariantContextTestProvider now tests that X = Y where X -> writing -> reading -> writing -> reading = Y for a variety of variant context inputs X
-- Added integration test reading 1000G SV chr1 calls (from Chris)
2012-07-19 16:14:26 -04:00
50365d01c4
Updated HSPTest expected values due to variant eval changes in earlier commit.
2012-07-19 15:24:53 -04:00
1592841c93
New function for merging nearby events into MNPs or complex substitutions. Added extensive unit tests.
2012-07-19 13:16:33 -04:00
a4884f82cd
Final final version of GATK beta license
2012-07-19 10:39:34 -04:00
c16f9f2f15
a) Use new method to check for GATK Like, b) minor improvements to indel pool caller (more to come): brain-dead, quick way to limit number of alt alleles to genotype. We can't process too many alt alleles because of the combinatorial explosion of GL values with high ploidy, and some STR validation targets had up to 12 alt alleles, resulting of GL vectors of > 1e8 elements. Can't use pileup elements since typically not many alleles will be in one pileup, and different alleles will appear in different samples, TBD a nicer solution. c) Commit to posterity scala script for large scale validation calling, still work in progress
2012-07-19 10:24:08 -04:00
5f5edeca63
Reverting move of BQSR tests to public, as per DR's email
2012-07-19 10:02:05 -04:00
e370030e6c
As requested by Mark, I've broken out the code to pull out the protected subclass when available (and otherwise use the public version) into the GATKLiteUtils class. People should use this code instead of reimplementing all of the java reflection on their own.
2012-07-18 22:44:37 -04:00
d46ccec04e
Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.
2012-07-18 21:48:58 -04:00
9c1ab1b0c0
Move BQSR integration test and its dependent files into public; previously there was a protected->private dependency.
2012-07-18 21:11:33 -04:00
Eric Banks
Mauricio Carneiro
Roger Zurawicki
Mark DePristo
Guillermo del Angel
Khalid Shakir
Ryan Poplin
Christopher Hartl