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96 Commits (f54c2ae3b4949a464ec2858524360a1c29405597)

Author SHA1 Message Date
Guillermo del Angel f54c2ae3b4 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-11 16:26:27 -04:00
Guillermo del Angel d587856f2d Private feature to input a list of family descriptions from a file and to look for MV's on all of these. Feature can also output a detailed description of the violation into a separate file 2011-07-11 14:17:59 -04:00
David Roazen a18380ab96 Merged bug fix from Stable into Unstable 2011-07-11 12:16:50 -04:00
David Roazen 8a78414432 Removed TileCovariate as a dependency for AnalyzeCovariates.jar 2011-07-11 12:10:11 -04:00
Guillermo del Angel 6e7b5e1e7a Merged bug fix from Stable into Unstable 
Merge branch 'master' into unstable
 2011-07-08 21:19:45 -04:00
Guillermo del Angel 7fbc5987d0 Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-07-08 21:17:32 -04:00
Mark DePristo bd29236684 Merge branch 'master' into diffengine 2011-07-08 14:08:17 -04:00
Guillermo del Angel 224574424e Bug fix: if we're genotyping a very long indel (>100 bp) fail gracefully instead of with an array out of bounds exception 2011-07-08 12:48:49 -04:00
Ryan Poplin 2a4b3ae4a2 Cleaning up / removing most of the monkeying around with annotation values that happens in VariantDataManager 2011-07-08 12:48:33 -04:00
Mark DePristo 8add2a3866 Merge branch 'master' into diffengine 2011-07-08 09:15:54 -04:00
Eric Banks cc143493e3 Merged bug fix from Stable into Unstable 2011-07-07 23:01:24 -04:00
Eric Banks 4cfe0dd857 Test for bad alleles so that we don't generate IndexOutOfBoundsExceptions 2011-07-07 23:01:03 -04:00
Mark DePristo 3d4f0e9dd7 Now supports the case where you have multiple AC values in the info field. 2011-07-07 17:21:15 -04:00
Ryan Poplin 212e9a1a0c Fixing unstable build after stable commit 2011-07-07 15:18:57 -04:00
Ryan Poplin 11d9a0473a Merged bug fix from Stable into Unstable 2011-07-07 15:03:58 -04:00
Ryan Poplin 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
Guillermo del Angel 4d565b0811 Merge branch 'incoming' 2011-07-07 06:21:05 -04:00
Guillermo del Angel 55c8c05060 Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-07 06:18:29 -04:00
Guillermo del Angel 5ab2e83904 a) Cosmetic modifications to IndelType annotation. b) Add ability to select samples from a file in PrintReads, c) fixes to shaped AF random selection in SelectVariants 2011-07-07 06:15:10 -04:00
Mark DePristo 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
Eric Banks 52f6f9fdcc Merged bug fix from Stable into Unstable 2011-07-06 16:05:48 -04:00
Eric Banks 54121eb082 Catch malformed bams that cause the writer to run in infinite loops 2011-07-06 16:05:08 -04:00
Eric Banks 76a01a7453 Merged bug fix from Stable into Unstable 2011-07-06 12:53:09 -04:00
Eric Banks 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
Ryan Poplin bdef233d4d Merged bug fix from Stable into Unstable 2011-07-06 10:05:02 -04:00
Ryan Poplin 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
Guillermo del Angel 8e8b901d12 Merged bug fix from Stable into Unstable 
Merge branch 'master' into unstable
 2011-07-06 09:57:55 -04:00
Guillermo del Angel 81a4d18468 Mark several indel-related arguments as @Hidden 2011-07-06 09:56:38 -04:00
Mauricio Carneiro 407a0e535f Merged bug fix from Stable into Unstable 2011-07-05 16:34:21 -04:00
Mauricio Carneiro 5298e3a942 Making the outputDir optional. Default = ./ 2011-07-05 16:30:41 -04:00
Mauricio Carneiro 7d3dfdfdf2 Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter. 2011-07-05 16:30:10 -04:00
Guillermo del Angel 9124c84a7c bug fixes 2011-07-04 21:10:44 -04:00
Guillermo del Angel bb85f232b9 bug fixes 2011-07-04 21:04:49 -04:00
Guillermo del Angel f26ffeaea0 bug fixes 2011-07-04 20:48:45 -04:00
Guillermo del Angel 04df153f47 bug fixes 2011-07-04 20:45:10 -04:00
Guillermo del Angel 7a04872a3f bug fixes 2011-07-04 20:33:59 -04:00
Guillermo del Angel 08bc843d4c SelectVariants can get a table to boost AF when choosing randomly 2011-07-04 20:23:22 -04:00
Mark A. DePristo 38740b0ff5 First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure. 2011-07-04 16:11:42 -04:00
Guillermo del Angel fac082de64 Report only highest AF and AC in multiallelic records in VariantsToTable or else R can't parse table 2011-07-03 14:32:12 -04:00
Guillermo del Angel abe9480c6d Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-02 21:19:15 -04:00
Ryan Poplin fb315b5f8c Merge branch 'incoming' 2011-07-02 18:10:48 -04:00
Ryan Poplin 41d46059e7 fixing bad format statement 2011-07-02 18:09:17 -04:00
Ryan Poplin 3804afeb8a Merge branch 'incoming' 2011-07-02 17:55:39 -04:00
Ryan Poplin 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
Ryan Poplin 6b8af6afd8 Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-02 17:15:56 -04:00
Ryan Poplin 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
Guillermo del Angel 09af6bbc6c Ugh - backed out experimental code not for public consumption unintendedly committed 2011-07-02 16:58:57 -04:00
Guillermo del Angel 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
Ryan Poplin 4532a84314 Merged bug fix from Stable into Unstable 2011-07-02 10:48:55 -04:00
Ryan Poplin 5faf40b79d Moving AnalyzeAnnotations into the archive because it has outlived its usefulness. 2011-07-02 10:39:53 -04:00