298dce2940
Adding the native jna support libraries from the jna.jar to the Queue package jar.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4965 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-08 10:48:30 +00:00
cd4883f4da
Be certain to include core GATK reference metadata features and codecs in the
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final package.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4892 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 21:30:07 +00:00
8101f8f301
Simplified the Queue package definition so that BCEL doesn't miss any dependent queue classes or those loaded via reflection.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4859 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 18:17:48 +00:00
e21a66d876
Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q.
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Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy.
Fixed the package definition of PipelineTest so that scalac won't recompile it every time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 15:29:40 +00:00
9f356b6cd0
Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4702 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 02:33:45 +00:00
fd78ce6c86
include the codecs into the RMD indexer that are available in the GATK, not just Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4649 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 06:35:04 +00:00
cb2e26a004
by request, an indexer tool to create Tribble style indexes outside of the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4632 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-06 18:59:06 +00:00
f5b66647ac
Include all standard annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4479 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-11 20:52:08 +00:00
c56c2641a8
/broad/1KG doesn't exist
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4435 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 12:54:38 +00:00
6448753cf7
Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4419 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-04 02:11:38 +00:00
575c38fc04
Accidental fail to commit missing file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4405 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-01 20:26:51 +00:00
fe2a0bb3a6
Fix for DoC issue with multiplexer -- will retire use of multiplexer when
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GATK reporting structure comes online.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4217 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-07 00:44:07 +00:00
cb74806bb5
Enabling support for any scala used in QScripts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4052 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-17 22:05:56 +00:00
b7c60b9729
Queue now uses its own version instead of the gatk version.
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Added a Queue release directory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4050 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-17 19:34:23 +00:00
307c8ca027
Created a new playground script for cleaning bams in Firehose.
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Some refactoring of Queue extensions for reusability in scripts.
Putting the extensions into the Queue.jar after building them.
More updates to GATK walker arguments specifying @Input and @Output for Queue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4032 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 23:52:24 +00:00
542d394e09
Cleaning up Queue debugging output.
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-l DEBUG with local programs now prints out the stdout/stderr of the programs as they are run.
More documentation in the examples with a new even simpler CountReads example.
Took out unused option to build Queue GATK extensions separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4025 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 15:54:08 +00:00
162febdef8
Added Queue packages, which must be run with 'ant queue package'.
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To assist with the above no longer removing jars during a new build, so 'ant queue dist' will still have the Queue.jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4020 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-12 17:45:53 +00:00
b5b2c19124
Updated resources package descriptor with dbsnp 129 for b37.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3916 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-03 02:42:48 +00:00
77cace3aff
It's probably a good idea to look carefully at what you've done before actually committing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3863 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 17:06:54 +00:00
44f9a631d6
Adding CombineVariants to release. Pining for the days when all of core/playground will be part of release by default...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3862 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 16:53:18 +00:00
ea117957b9
Add CountFunctionalVariants to local release (for firehose)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3814 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-17 01:36:16 +00:00
c1ecf75dd5
Update to the latest rev of the picard sharding patch. Includes updates reflecting
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the imminent move of IlluminaUtil into picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 20:33:21 +00:00
2014837f8a
VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3458 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 18:20:18 +00:00
42fa12d9e4
without the *, the package system only took directly referenced files (which pulled in VCF and BED) but skipped dbsnp. Epic star fail...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3423 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-24 05:19:57 +00:00
7910a6a7cb
adding all of Tribble, not just select codecs, to the package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3411 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 15:48:50 +00:00
3b52ac67e0
adding the Tribble codecs to the package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3315 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 21:06:15 +00:00
0e58fb7cc0
Moved over to be a walker inside the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3313 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:28:03 +00:00
1a99fb9318
First pass at liftover tool. Passing buck over to Aaron...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3306 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 20:38:19 +00:00
3db73e0791
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3221 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 03:00:43 +00:00
bbb83859cd
Adding VE modules to package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3185 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 14:44:06 +00:00
2ca1849df9
Adding HaplotypeScore to the VariantAnnotator package (so it can be used with Firehose)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3171 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 18:37:21 +00:00
8017fb123f
changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3116 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 20:55:19 +00:00
5a3622b051
Get rid of CoverageStatistics from packages so ant package doesn't go looking for it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3115 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 18:04:33 +00:00
699a0ea9d1
adding SequenomValidationConvertor and VariantsToVCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3113 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 17:27:42 +00:00
3330666780
Add CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3092 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 15:45:53 +00:00
85037ab13f
Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of
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Picard patch, including move of some of the Picard private classes we use to Picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 03:21:27 +00:00
bb7e0c27fd
updating the package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3045 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:42:31 +00:00
740238b4fa
removing a reference to the VCFValidator, which is gone.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2986 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 21:32:17 +00:00
91b3f9745e
removing the package description for the VCF validator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2910 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 15:45:51 +00:00
9306041cf4
Since IntervalCleaner is gone for good, it is sensible to update the package to refer to the new IndelRealigner instead
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2883 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 16:42:56 +00:00
3738b76320
Added a playground concordance analyzer for summarizing VariantEval across a group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2867 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 20:28:52 +00:00
280f38f635
Bringing IndelGenotyper back to life
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2770 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-03 20:12:49 +00:00
ed23e54abd
Added VariantEval to the GATK release. Woo hoo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2763 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-02 02:38:39 +00:00
4642a1ae59
Give the symlink on the webserver a name that would be a bit more obvious.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2717 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-28 00:40:20 +00:00
eccf40b17d
Tweak the layout of the resulting .tar.bz2 a bit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2714 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 22:07:37 +00:00
668defc841
Fix the dreaded 'can't use fully qualified symlinks on the ftp server' gotcha.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2710 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 20:55:48 +00:00
8453676b71
added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine.
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Also deleted the FixBamSortOrder package that isn't used anymore.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2701 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 05:17:01 +00:00
bbddeb693f
Updated the package to use RealignerTargetCreator. Also, removed IndelGenotyper since it's still experimental.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2698 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 03:45:15 +00:00
169032aa78
Add new 'release' task to push releases into a shared directory and the website.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2695 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 22:50:20 +00:00
31d252c0a1
Now using the new VariantEval package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2689 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 16:32:44 +00:00
kshakir
hanna
aaron
ebanks
chartl
rpoplin
asivache