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
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
938017d887
Removed ReadQualityRecalibrator.xml
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2226 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:14:14 +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
bc8f3d58ae
Added an aligner package to make it easier for people to use outside the GATK.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2206 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 23:04:10 +00:00
d563f4bd2c
Add IlluminaUtil to picard-private.jar
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2161 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:25:21 +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
4082f4677e
Picard-private with classes for reading Picard dbSNP binary file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2086 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:24:28 +00:00
8eff1cc436
Extract and include only the Tim Fennell-approved parts of picard private.
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Hopefully this is a temporary solution and these classes will be migrated
into picard-public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2041 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:42:33 +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
3928751bf5
Fail for missing resource files / scripts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1692 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 21:31:01 +00:00
eebe2978a1
Add code to fail if any of the classes explicitly listed as a dependency is not found. Will still *not* fail if a package or script or resource file is missing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1691 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 21:22:27 +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
026e09ec07
adding the package description for the VCF validator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1444 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-20 04:46:27 +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
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
af7a759ba4
Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1050 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:29:30 +00:00
f45d5a73a5
Package annotator for Alec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1038 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 22:40:40 +00:00
ed7fac1c90
Add bcel and cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1032 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 19:28:04 +00:00
e2ccea4883
Cleanup. Move output of packaging to dist directory. Don't always create resources directory. Make jar take on the package name.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1023 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:47:23 +00:00
hanna
kshakir
rpoplin
ebanks
aaron
alecw
asivache
depristo