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
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
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
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
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
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
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
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
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
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
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
ac3895c218
Update the location of the DepthOfCoverage tool in the packaging system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2250 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 19:11:53 +00:00
608fa4cc3a
Update packaging system to produce multiple jars if asked nicely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2246 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:11:12 +00:00
93842abb4a
Let the packages know about the changes made for AnalyzeCovariates.jar
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2222 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:09:53 +00:00
7055a3ea2d
- All annotations are now required to return their VCF INFO keys and descriptions
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- Renamed keys to fit with the standard naming
- FisherStrand is no longer standard
- Integration tests no longer test experimental annotations since they're not stable
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2216 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:24:06 +00:00
fe8809d12a
Added Covariate classes to the Early Access binary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2159 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 18:59:21 +00:00
e8bb88e33d
Updated package for early access
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2158 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 18:08:12 +00:00
ef00ba3ced
added IndelGenotyperV2Walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1937 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 20:07:31 +00:00
a8a2c1a2a1
Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1882 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 01:19:58 +00:00
aec61c558b
moving IndelGenotyper out from playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1731 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 19:43:53 +00:00
db9390811a
Package tool doesn't provide an error if classes listed in the package are not found, and classes were moved from playground to core.
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This step: correct the classes listed in the package.
Next step: update the packaging tool to fail if class is not found.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1680 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 15:06:45 +00:00
8f9dd03e87
Get rid of unnecessary files for generating recalibration data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1626 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 15:53:06 +00:00
e6827424b9
Added support python and R scripts for generating covariate output graphs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1625 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 14:17:36 +00:00
f3f5e849cb
SSG now in early access
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1581 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 16:45:19 +00:00
eb664ae287
Added VariantFiltrationWalker to GATK early release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1502 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 02:17:50 +00:00
e2ec703a32
Added indel cleaner and quality scores recalibrator to the GATK package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1311 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 16:20:38 +00:00
5d1345539d
Packaging cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1242 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 21:00:02 +00:00
25365ccb07
Adding more walkers to the base GATK package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1241 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 20:40:52 +00:00
d0cef5ff9d
Oops. Specified incorrect classname in packgae for depth of coverage walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1161 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 21:40:40 +00:00
62807139fc
Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1159 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:54:01 +00:00
6570ce0b5b
added the example files to the distro
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1152 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 23:16:42 +00:00
e93f751bd7
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 21:59:54 +00:00
29df74ae23
Plumbed packaging support into build.xml and added package for GATK.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 19:41:16 +00:00
rpoplin
aaron
chartl
ebanks
asivache
hanna
alecw
depristo