Ami Levy-Moonshine
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d3c2c97fb2
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Merge branch 'master' of github.com:broadinstitute/gsa-unstable
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2013-01-06 23:35:47 -05:00 |
Eric Banks
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8822b8e7c8
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Moving HelpConstants out of HelpUtils so that we stop getting these ProgramElementDoc errors when com.sun.javadoc cannot load on a user's system.
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2013-01-06 14:30:45 -05:00 |
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Ami Levy-Moonshine
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6590039bc3
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add fast gather to UG; change UG to work with log-lessHMM (work in prograss)
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2012-12-20 14:58:57 -05:00 |
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Eric Banks
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e199562c25
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I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).
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2012-11-27 10:26:17 -05:00 |
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 |
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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 |