Guillermo del Angel
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224574424e
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Bug fix: if we're genotyping a very long indel (>100 bp) fail gracefully instead of with an array out of bounds exception
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2011-07-08 12:48:49 -04:00 |
Ryan Poplin
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2a4b3ae4a2
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Cleaning up / removing most of the monkeying around with annotation values that happens in VariantDataManager
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2011-07-08 12:48:33 -04:00 |
Christopher Hartl
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f7d188232f
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Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-08 12:32:32 -04:00 |
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Christopher Hartl
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f7b7467139
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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!)
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2011-07-08 12:28:46 -04:00 |
Mark DePristo
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8add2a3866
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Merge branch 'master' into diffengine
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2011-07-08 09:15:54 -04:00 |
Eric Banks
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9a14b914b7
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Not sure why this happened...
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2011-07-07 23:09:12 -04:00 |
|
Eric Banks
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5ed7243b64
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Removing old oneoffs walkers as I threatened
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2011-07-07 23:02:41 -04:00 |
|
Eric Banks
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cc143493e3
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Merged bug fix from Stable into Unstable
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2011-07-07 23:01:24 -04:00 |
|
Eric Banks
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4cfe0dd857
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Test for bad alleles so that we don't generate IndexOutOfBoundsExceptions
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2011-07-07 23:01:03 -04:00 |
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Mark DePristo
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b9ffe592c4
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Now supports files without indels calls in them
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2011-07-07 22:32:47 -04:00 |
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Mark DePristo
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609ca0baab
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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.
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2011-07-07 22:02:45 -04:00 |
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Mark DePristo
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3d4f0e9dd7
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Now supports the case where you have multiple AC values in the info field.
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2011-07-07 17:21:15 -04:00 |
Menachem Fromer
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adb6fc910e
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Merged bug fix from Stable into Unstable
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2011-07-07 16:24:57 -04:00 |
|
Menachem Fromer
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ce5a1c2cbe
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Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
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2011-07-07 16:21:27 -04:00 |
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Menachem Fromer
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1a42a5b4ec
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Refactored oneoffs to properly be in the private package
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2011-07-07 16:16:12 -04:00 |
Kiran V Garimella
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58c841ce1b
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Merged bug fix from Stable into Unstable
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2011-07-07 16:15:57 -04:00 |
|
Kiran V Garimella
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13519c2c3d
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Moved PhaseByTransmission per Eric's request
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2011-07-07 16:14:14 -04:00 |
|
Guillermo del Angel
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231e4bdb11
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Merged bug fix from Stable into Unstable
Merge branch 'master' into unstable
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2011-07-07 15:41:01 -04:00 |
|
Guillermo del Angel
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06f12eca56
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Move from qscript/delangel to qscripts/calling
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2011-07-07 15:39:48 -04:00 |
|
Guillermo del Angel
|
d344317f8b
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Merged bug fix from Stable into Unstable
Merge branch 'master' into unstable
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2011-07-07 15:27:35 -04:00 |
|
Guillermo del Angel
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8a571e3488
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Move IndelCountCovariates package to gatk.walkers
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2011-07-07 15:25:37 -04:00 |
|
Ryan Poplin
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212e9a1a0c
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Fixing unstable build after stable commit
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2011-07-07 15:18:57 -04:00 |
|
Ryan Poplin
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11d9a0473a
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Merged bug fix from Stable into Unstable
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2011-07-07 15:03:58 -04:00 |
|
Ryan Poplin
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50111db2b7
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Fixing non-determinism in single-threaded VQSR by moving references to cern.Normal over to the static random generator available in GenomeAnalysisEngine
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2011-07-07 15:02:48 -04:00 |
|
Ryan Poplin
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fe8e2c305c
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Adding dev qscript which I used to perform the VQSR in exome by sample size experiment
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2011-07-07 13:37:29 -04:00 |
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Mark DePristo
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0df31f3d78
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Simple usability improvements to the DiffEngine and DiffObjectsWalker. Can specify min count for summarized diff objects for display.
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2011-07-07 11:16:42 -04:00 |
|
Mark DePristo
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ccf34f7e45
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(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!
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2011-07-06 21:57:22 -04:00 |
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Eric Banks
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52f6f9fdcc
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Merged bug fix from Stable into Unstable
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2011-07-06 16:05:48 -04:00 |
|
Eric Banks
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54121eb082
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Catch malformed bams that cause the writer to run in infinite loops
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2011-07-06 16:05:08 -04:00 |
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Christopher Hartl
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3ed6d494ce
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Huh, guess I forgot to commit this one.
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2011-07-06 15:58:12 -04:00 |
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Christopher Hartl
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ebf117f1fe
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Change packages to reflect current structure. Remove @Overrides on interface methods.
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2011-07-06 14:05:50 -04:00 |
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Eric Banks
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76a01a7453
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Merged bug fix from Stable into Unstable
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2011-07-06 12:53:09 -04:00 |
|
Eric Banks
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14fee4ccbd
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Patch from Bob to deal with symbolic alleles: these weren't getting padded but they should be.
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2011-07-06 12:51:44 -04:00 |
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Christopher Hartl
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a5ad603b35
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Gah. Missed one.
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2011-07-06 12:15:41 -04:00 |
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Christopher Hartl
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759bc25643
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Get rid of the dumb backups
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2011-07-06 12:15:04 -04:00 |
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Christopher Hartl
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f5890b1715
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Moving RFA from string/walkers to sting/gatk/walkers (PSP2 as well). Dumb emacs backups committed accidentally, will be removed shortly.
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2011-07-06 12:12:25 -04:00 |
Khalid Shakir
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515553c801
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Merged bug fix from Stable into Unstable
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2011-07-06 11:34:13 -04:00 |
|
Khalid Shakir
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0b86958a56
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Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/stable
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2011-07-06 11:33:15 -04:00 |
|
Khalid Shakir
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c93d0b37a8
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Fixed namespace of the pipeline classes.
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2011-07-06 11:32:46 -04:00 |
|
Ryan Poplin
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bdef233d4d
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Merged bug fix from Stable into Unstable
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2011-07-06 10:05:02 -04:00 |
|
Ryan Poplin
|
e8ed6b7f0f
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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
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8e8b901d12
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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
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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
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7b699f8b17
|
Switched GridEngine from looking from environment variable to using embedded jar.
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2011-07-05 21:59:00 -04:00 |
Mauricio Carneiro
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407a0e535f
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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
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7d3dfdfdf2
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Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
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2011-07-05 16:30:10 -04:00 |
|
Mark A. DePristo
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080875d5da
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Refactored DiffNode/DiffElement/DiffValue class structure. DiffElement is now a pair of Name -> Value, where value is either a DiffValue or its subclass DiffNode. Code cleaned up, more tests added. DiffEngine is now working, with tests. DiffObjectWalker can now take two VCFs and itemize the difference between the two files correctly and concisely.
|
2011-07-05 16:13:39 -04:00 |
|
Mauricio Carneiro
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a765c08381
|
New home for the ReducedBAMEvaluation qscript.
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2011-07-05 13:58:50 -04:00 |