a1b4cafe7a
Bug fix for NPE when timer wasn't initialized
2011-09-20 13:59:59 -04:00
b7511c5ff3
Fixed long-standing bug in tribble index creation
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-- Previously, on the fly indices didn't have dictionary set on the fly, so the GATK would read, add dictionary, and rewrite the index. This is now fixed, so that the on the fly index contains the reference dictionary when first written, avoiding the unnecessary read and write
-- Added a GenomeAnalysisEngine and Walker function called getMasterSequenceDictionary() that fetches the reference sequence dictionary. This can be used conveniently everywhere, and is what's written into the Tribble index
-- Refactored tribble index utilities from RMDTrackBuilder into IndexDictionaryUtils
-- VCFWriter now requires the master sequence dictionary
-- Updated walkers that create VCFWriters to provide the master sequence dictionary
2011-09-20 10:53:18 -04:00
230e16d7c0
Merge branch 'master' into rodrewrite
2011-09-20 06:54:18 -04:00
b507bd946c
Merged bug fix from Stable into Unstable
2011-09-20 00:18:16 -04:00
61b89e236a
To work around potential problem with invalid javax.mail 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code to remove 1.4.1.
2011-09-20 00:14:35 -04:00
aa8afa3899
Merge
2011-09-19 21:16:47 -04:00
56106d54ed
Changing ReadUtils behavior to comply with GenomeLocParser
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Now the functions getRefCoordSoftUnclippedStart and getRefCoordSoftUnclippedEnd will return getUnclippedStart if the read is all contained within an insertion. Updated the contracts accordingly. This should give the same behavior as the GenomeLocParser now.
2011-09-19 14:00:00 -04:00
080c957547
Fixing contracts for SoftUnclippedEnd utils
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Now accepts reads that are entirely contained inside an insertion.
2011-09-19 13:53:53 -04:00
ba150570f3
Updating to use new rod system syntax plus name change for CountRODs
2011-09-19 13:30:32 -04:00
5e832254a4
Fixing ReadAndInterval overlap comments.
2011-09-19 13:28:41 -04:00
ecb8466662
Merged bug fix from Stable into Unstable
2011-09-19 12:32:08 -04:00
8143def292
Fix the -T argument in the DepthOfCoverage docs
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Add documentation for the RefSeqCodec, pointing users to the wiki page describing how to create the file
2011-09-19 12:31:47 -04:00
095f75ff7d
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-19 12:24:12 -04:00
85626e7a5d
We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too.
2011-09-19 12:24:05 -04:00
034b868588
Revert "Fix the -T argument in the DepthOfCoverage docs"
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This reverts commit 0994efda998cf3a41b1a43696dbc852a441d5316.
2011-09-19 12:16:07 -04:00
cfde0e674b
Merge branch 'sgintervals'
2011-09-19 12:02:41 -04:00
3e93f246f7
Support for sample sets in AssignSomaticStatus
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-- Also cleaned up SampleUtils.getSamplesFromCommandLine() to return a set, not a list, and trim the sample names.
2011-09-19 11:40:45 -04:00
41ffb25b74
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-19 10:55:18 -04:00
ca1b30e4a4
Fix the -T argument in the DepthOfCoverage docs
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Add documentation for the RefSeqCodec, pointing users to the wiki page describing how to create the file
2011-09-19 10:29:06 -04:00
4ad330008d
Final intervals cleanup
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-- No functional changes (my algorithm wouldn't work)
-- Major structural cleanup (returning more basic data structures that allow us to development new algorithm)
-- Unit tests for the efficiency of interval partitioning
2011-09-19 10:19:10 -04:00
6ea57bf036
Merge branch 'master' into sgintervals
2011-09-19 09:50:19 -04:00
6bd42c053d
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-18 20:18:39 -04:00
bed78b47e0
Marginally better formating, with hours the default time
2011-09-18 20:18:18 -04:00
7fa1e237d9
Forgot to git stash pop new MD5's for CombineVariants integration test
2011-09-16 12:53:54 -04:00
e7b9a009b7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-16 12:48:30 -04:00
42f3b7ba32
Merged bug fix from Stable into Unstable
2011-09-16 12:46:38 -04:00
33967a4e0c
Fixed issue reported by chartl where cloned functions lost tags on @Inputs.
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Updated ExampleUnifiedGenotyper.scala with new syntax.
2011-09-16 12:46:07 -04:00
92f7db3228
Can now optionally suppress the use of all annotations and then add back in specific annotations/groups. This was necessary, since using all annotations for VariantAnnotator NOW includes SNPeff, which (annoyingly) requires a SNPeff VCF...
2011-09-16 02:40:24 -04:00
b2e8e11128
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-16 00:52:27 -04:00
3cd9f3fe81
Merge remote-tracking branch 'unstable/master'
2011-09-15 21:14:17 -04:00
57b3efa2e2
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 21:06:38 -04:00
939babc820
Updating formating for ValidationAmplicons GATK docs
2011-09-15 21:05:51 -04:00
9fdf1f8eb6
Fix some doc formatting for Depth of Coverage
2011-09-15 21:05:22 -04:00
e6e9b08c9a
Must provide alleles VCF to UGCallVariants
2011-09-15 18:51:09 -04:00
1960bcabb8
Updated to use new ROD-binding system
2011-09-15 18:07:32 -04:00
d78e00e5b2
Renaming VariantAnnotator SnpEff keys
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This is to head off potential confusion with the output from the SnpEff tool itself,
which also uses a key named EFF.
2011-09-15 17:42:15 -04:00
1971fb35d7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 16:55:33 -04:00
9dc6354130
Oops didn't mean to touch this test before
2011-09-15 16:55:24 -04:00
2a8b8efd2f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 16:26:35 -04:00
2f58fdb369
Adding expected output doc to CountCovariates
2011-09-15 16:26:11 -04:00
fd1831b4a5
Updating docs to include more details
2011-09-15 16:25:03 -04:00
6d02a34bfb
Updating docs to include output
2011-09-15 16:17:54 -04:00
4ef6a4598c
Updating docs to include output
2011-09-15 16:10:34 -04:00
fe474b77f8
Updating docs so printing looks nicer
2011-09-15 16:05:39 -04:00
f04e51c6c2
Adding docs from Andrey since his repo was all screwed up.
2011-09-15 15:38:56 -04:00
ce73dc4071
Update to the bindings for liftOverVCF.pl (to -V from -B)
2011-09-15 15:33:09 -04:00
7d6b34b1bb
Can now optionally annotate with a dbSNP VCF
2011-09-15 15:31:38 -04:00
86480b2e13
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 15:31:07 -04:00
04f5723399
Updated to use new ROD-binding system
2011-09-15 14:28:06 -04:00
d369d10593
Adding documentation before the release for GATK wiki page
2011-09-15 13:56:23 -04:00
Mark DePristo
Khalid Shakir
Mauricio Carneiro
Eric Banks
Christopher Hartl
Guillermo del Angel
Menachem Fromer
David Roazen
Ryan Poplin