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6534 Commits (5e0fe2d0f976aceb1aac53ea0d8db09bccd7633c)

Author SHA1 Message Date
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
Christopher Hartl f7d188232f Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-08 12:32:32 -04:00
Christopher Hartl f7b7467139 Moving the private filter package from sting/filters to sting/gatk/filters, updating package name and imports. This was preventing walkers from running. (Thanks, Matt!) 2011-07-08 12:28:46 -04:00
Mark DePristo 8add2a3866 Merge branch 'master' into diffengine 2011-07-08 09:15:54 -04:00
Eric Banks 9a14b914b7 Not sure why this happened... 2011-07-07 23:09:12 -04:00
Eric Banks 5ed7243b64 Removing old oneoffs walkers as I threatened 2011-07-07 23:02:41 -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 b9ffe592c4 Now supports files without indels calls in them 2011-07-07 22:32:47 -04:00
Mark DePristo 609ca0baab canRead() now implemented by looking for BAM_MAGIC value BAM\1 in file, and for the ##fileformat=VCFv4 header line in the VCF file. BAM reader now fully operational, and with a unit test. All unit tests work now. Minus function / class documentation the system is pretty stable and usable. 2011-07-07 22:02:45 -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
Menachem Fromer adb6fc910e Merged bug fix from Stable into Unstable 2011-07-07 16:24:57 -04:00
Menachem Fromer ce5a1c2cbe Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-07-07 16:21:27 -04:00
Menachem Fromer 1a42a5b4ec Refactored oneoffs to properly be in the private package 2011-07-07 16:16:12 -04:00
Kiran V Garimella 58c841ce1b Merged bug fix from Stable into Unstable 2011-07-07 16:15:57 -04:00
Kiran V Garimella 13519c2c3d Moved PhaseByTransmission per Eric's request 2011-07-07 16:14:14 -04:00
Kiran V Garimella d540d93d93 Moved PhaseByTransmission from walkers to gatk.walkers 2011-07-07 15:46:27 -04:00
Guillermo del Angel 231e4bdb11 Merged bug fix from Stable into Unstable 
Merge branch 'master' into unstable
 2011-07-07 15:41:01 -04:00
Guillermo del Angel 06f12eca56 Move from qscript/delangel to qscripts/calling 2011-07-07 15:39:48 -04:00
Guillermo del Angel d344317f8b Merged bug fix from Stable into Unstable 
Merge branch 'master' into unstable
 2011-07-07 15:27:35 -04:00
Guillermo del Angel 8a571e3488 Move IndelCountCovariates package to gatk.walkers 2011-07-07 15:25:37 -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
Ryan Poplin fe8e2c305c Adding dev qscript which I used to perform the VQSR in exome by sample size experiment 2011-07-07 13:37:29 -04:00
Mark DePristo 0df31f3d78 Simple usability improvements to the DiffEngine and DiffObjectsWalker. Can specify min count for summarized diff objects for display. 2011-07-07 11:16:42 -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
Christopher Hartl 3ed6d494ce Huh, guess I forgot to commit this one. 2011-07-06 15:58:12 -04:00
Christopher Hartl ebf117f1fe Change packages to reflect current structure. Remove @Overrides on interface methods. 2011-07-06 14:05:50 -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
Christopher Hartl a5ad603b35 Gah. Missed one. 2011-07-06 12:15:41 -04:00
Christopher Hartl 759bc25643 Get rid of the dumb backups 2011-07-06 12:15:04 -04:00
Christopher Hartl f5890b1715 Moving RFA from string/walkers to sting/gatk/walkers (PSP2 as well). Dumb emacs backups committed accidentally, will be removed shortly. 2011-07-06 12:12:25 -04:00
Khalid Shakir 515553c801 Merged bug fix from Stable into Unstable 2011-07-06 11:34:13 -04:00
Khalid Shakir 0b86958a56 Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/stable 2011-07-06 11:33:15 -04:00
Khalid Shakir c93d0b37a8 Fixed namespace of the pipeline classes. 2011-07-06 11:32:46 -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
Mark A. DePristo 1f1231f47a Implementation of key summarizing algorithm and support routines. UnitTests for support routines. Almost ready to test the summarizer on real difference set. 2011-07-05 23:23:49 -04:00
Khalid Shakir 7b699f8b17 Switched GridEngine from looking from environment variable to using embedded jar. 2011-07-05 21:59:00 -04:00
Mauricio Carneiro 407a0e535f Merged bug fix from Stable into Unstable 2011-07-05 16:34:21 -04:00