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
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
93dc2cdc70
Start of a 'package' format for xml files which should be distributed together.
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Uses xslt scripts to transform packages into build scripts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1005 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 00:52:48 +00:00
rpoplin
ebanks
hanna
alecw
asivache
depristo
aaron