kshakir
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213cc00abe
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Refactored argument matching to support other plugins in addition to file lists.
Added plugin support for sending Queue status messages.
Argument parsing can store subclasses of java.io.File, for example RemoteFile.
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2012-10-15 15:10:45 -04:00 |
Mauricio Carneiro
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d446d34227
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GATK Error messages now point to the new website instead of GetSatisfaction.
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2012-07-20 17:27:11 -04:00 |
Eric Banks
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4c730542f0
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Handle RuntimeExceptions thrown by Picard that are really User Errors. I will add unit tests for these as best I can later.
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2012-07-18 13:56:35 -04:00 |
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Eric Banks
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5821c11fad
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For BAM and Reviewed errors we now check the error message to see if it's actually a 'too many open files' problem and, if so, we generate a User Error instead.
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2011-11-22 10:50:22 -05:00 |
Matt Hanna
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8bb4d4dca3
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First pass of the asynchronous block loader.
Block loads are only triggered on queue empty at this point. Disabled by
default (enable with nt:io=?).
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2011-11-18 15:02:59 -05:00 |
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Khalid Shakir
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89a581a66f
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Added ability to specify arguments in files via -args/--arg_file
Pushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()
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2011-10-24 15:58:34 -04:00 |
Mark DePristo
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6fa17d86ae
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Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator
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2011-07-21 00:18:07 -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 |
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 |