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
3380b6ebe8
Clean up packaging in preparation for actually releasing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2686 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 03:12:49 +00:00
648a36d08e
Temporary solution: add the commons logging implementation to the VariantFiltration package. Downstream solution is described in GSA-262.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2665 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 01:46:18 +00:00
e00cb688ac
Cleanup of GATK-GSA-Pipeline to support the new naming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2658 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 22:17:35 +00:00
de21943acd
A few more bug fixes based on extended testing. Sorry, Eric.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2656 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 22:12:16 +00:00
4fc926232c
More cleanup. Make sure resources are unioned among all the specified modules.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2653 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 19:38:46 +00:00
3e54e131e0
Cleanup and formatting overhaul.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 19:22:56 +00:00
ee421c106c
Autogenerate .tar.bz2 with embedded version number. Misc formatting changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2651 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 18:32:46 +00:00
2261f57e5c
Rename modules to reflect the fact that they're really packages in their own right.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2638 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 01:13:17 +00:00
2f3fbc145d
A rethink of some of the modules from last night -- make the modules stand alone.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2637 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 00:59:21 +00:00
96a053c769
Port VariantEval and FindContaminatingReadGroups to modules.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2634 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 22:10:33 +00:00
e936cbff1b
Removed experimental recalibration covariates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2631 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:29:43 +00:00
e1fba42fdb
Add new 'module' XML tag, that can import modules from supplementary files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2624 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 01:56:04 +00:00
a57886ab81
Adding VCFValidator to package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2619 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-17 03:39:05 +00:00
aa08c82ac0
Removed experimental covariates and added standard annotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2617 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-17 02:17:32 +00:00
420cef4094
Added version numbers to the help doclet extractor. Since the help system is behaving
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more like a resource bundle at this point, changed it over to use the Java ResourceBundle
support classes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2606 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 23:31:29 +00:00
d30e2b390a
Remove several walkers that won't be used in the GATK-GSA-Pipeline.jar.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2602 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 21:17:23 +00:00
d2f752dbc1
Adding TileCovariate to the GATK-GSA-Pipeline list.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2598 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 20:57:13 +00:00
190335db9c
Added a GSA specific package with Playground walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2597 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 20:50:29 +00:00
f2e539c52f
As per discussions with Tim we are reverting the previous change regarding PairedReadOrderCovariate. The CycleCovariate now differentiates between first and second of pair by multiplying the cycle by -1. PairedReadOrderCovariate has been removed completely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2592 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 18:18:59 +00:00
2a116bb5d6
Made the VCF validator a simple rod walker instead of having it be in a separate package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2588 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 06:39:06 +00:00
9f89c62c75
Added b37 reference files and dbsnp 130 rods to resources
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2578 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 03:28:22 +00:00
49c44e7b36
PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2574 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 20:09:10 +00:00
f587ff46af
Tile is now a standard covariate. By default the TileCovariate returns -1 if tile can't be derived from the read's name. Added a new command line option -throwTileException which will force TileCovariate to throw an exception if tile can't be derived for a read. Singleton covariates, such as any read group without tile info, must be skipped over in TableRecalibration so that the sequential formulation doesn't apply the same correction more than once. TileCovariate class has been added to the Early Access package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2544 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 22:51:41 +00:00
66eeb4a552
Adding a package description for making a version of the GATK that only includes the FixBAMSortOrderTag walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2426 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 00:35:24 +00:00
c0c9f6c8b6
Create package that contains just what Picard needs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2421 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 18:48:27 +00:00
aa86f3710d
Updating HomopolymerCovariate to only count the consecutive previous bases. I left in the code but commented out for if somebody wants to worry about carry forward homopolymer problems.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2391 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 18:25:09 +00:00
9143822822
Fix half-hearted attempt to try to move classes from package to package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2389 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 17:41:42 +00:00
717eb1de96
- Depth annotation now includes MQ0 reads
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- Removed MQ0 annotation
- Updated RMS MQ annotation to use new pileup
- UG now outputs all of its arguments as key/value pairs in the header (for VCF)
- Cleaned up VCFGenotypeWriterAdapter interface a bit
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 02:53:00 +00:00
2cf21317f9
Create package that contains just what Picard needs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2282 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 21:22:07 +00:00
c9e385f541
Add TileCovariate to GenomeAnalysisTK package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2277 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 16:39:59 +00:00
chartl
aaron
ebanks
hanna
asivache
kshakir
rpoplin
alecw