Ryan Poplin
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894d3340be
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Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.
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2012-02-03 17:13:52 -05:00 |
Khalid Shakir
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b80d407dc7
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
Other minor cleanup.
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2011-10-27 14:17:07 -04:00 |
Guillermo del Angel
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1c485d8b5e
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Forgot that no matter how trivial a change it's a good idea to compile first
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2011-10-11 11:18:41 -04:00 |
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Guillermo del Angel
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1975de1b32
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Second try: hide --do_indel_quality in AnalyzeCovariates
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2011-10-11 11:11:29 -04:00 |
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Guillermo del Angel
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6506ea83e8
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Revert "Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users"... a hidden passenger change made it through.
This reverts commit 70e10ccb1be90dcff8f4485ae6ee036db2d1ac86.
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2011-10-11 11:03:12 -04:00 |
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Guillermo del Angel
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4c1d8c8d44
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Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users
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2011-10-11 11:01:06 -04:00 |
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Ryan Poplin
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2585fc3d6c
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Updating Rscript path doc text for Broad users
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2011-09-21 15:22:26 -04:00 |
Mark DePristo
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ccec0b4d73
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AnalyzeCovariates uses the general RScript system now
-- Convenience constructor for collection for testing
-- callRScript() now accepts Objects not Strings, for convenience
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2011-08-27 12:54:13 -04:00 |
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Ryan Poplin
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7c4ce6d969
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Added GATKDocs for the VQSR walkers.
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2011-08-18 14:00:39 -04:00 |
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Ryan Poplin
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bb79d3edae
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Added GATKDocs for the BQSR walkers.
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2011-08-18 10:57:48 -04:00 |
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Mark DePristo
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9992c373be
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Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
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2011-07-17 20:29:58 -04:00 |
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Ryan Poplin
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e8ed6b7f0f
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Adding more comments to main VQSR walker. Fixing copyright lines. Bug fix for default paths to now point to public/R/ instead of R/ Bug fix in VQSR for the path to the R scripts not ending in a slash.
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2011-07-06 10:01:14 -04:00 |
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 |