Khalid Shakir
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b090751f62
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Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.
Updates to HybridSelectionPipeline:
- Added annotations back via snpEff
- Minor updates to VQSR paths and lowered memory
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2011-09-27 14:33:57 -04:00 |
Matt Hanna
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059cdcb1be
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Changing packaging system path for GATK-only Tribble codecs.
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2011-09-26 14:58:19 -04:00 |
Eric Banks
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5e06a45628
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Fix the AnalayzeCovariates packaging.
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2011-09-22 11:55:40 -04:00 |
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Eric Banks
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4e116760f4
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Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates.
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2011-09-12 15:09:25 -04:00 |
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Khalid Shakir
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1f8fc4a041
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Added edu.mit.broad.picard to Queue packaged jar.
Added hack to workaround EDU.oswego namespace and staging on mac case-insensitive filesystems.
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2011-07-23 14:40:29 -04:00 |
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Khalid Shakir
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9b446020f9
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Using picard implementations for accessing aggregation directories.
Added more utilities to PicardPrivate.
Revved picard.
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2011-07-18 21:49:03 -04:00 |
David Roazen
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8a78414432
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Removed TileCovariate as a dependency for AnalyzeCovariates.jar
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2011-07-11 12:10:11 -04:00 |
Ryan Poplin
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5faf40b79d
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Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.
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2011-07-02 10:39:53 -04:00 |
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Khalid Shakir
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b6bc64a0c8
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Cleanup of the utils.broad package.
Using Picard IoUtils on sample names.
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2011-07-01 20:47:03 -04:00 |
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David Roazen
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4b17f34640
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Fixes to the packaging system to work with the new directory structure.
Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
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2011-06-30 18:27:17 -04:00 |
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David Roazen
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3c9497788e
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Reorganized the codebase beneath top-level public and private directories,
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
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2011-06-28 06:55:19 -04:00 |