aa99a5f47c
Added an option to print out the version string
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@argument (-)-version
(should this be @hidden?)
Prints out the version to System.out and quit(0)
No tests. (any ideas on how to test this would be happily accepted)
2013-02-15 12:42:59 -05:00
2a4ccfe6fd
Updated all JAVA file licenses accordingly
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GSATDG-5
2013-01-10 17:06:41 -05:00
d3c2c97fb2
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-06 23:35:47 -05:00
8822b8e7c8
Moving HelpConstants out of HelpUtils so that we stop getting these ProgramElementDoc errors when com.sun.javadoc cannot load on a user's system.
2013-01-06 14:30:45 -05:00
6590039bc3
add fast gather to UG; change UG to work with log-lessHMM (work in prograss)
2012-12-20 14:58:57 -05:00
e199562c25
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).
2012-11-27 10:26:17 -05:00
213cc00abe
Refactored argument matching to support other plugins in addition to file lists.
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Added plugin support for sending Queue status messages.
Argument parsing can store subclasses of java.io.File, for example RemoteFile.
2012-10-15 15:10:45 -04:00
d446d34227
GATK Error messages now point to the new website instead of GetSatisfaction.
2012-07-20 17:27:11 -04:00
4c730542f0
Handle RuntimeExceptions thrown by Picard that are really User Errors. I will add unit tests for these as best I can later.
2012-07-18 13:56:35 -04:00
5821c11fad
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.
2011-11-22 10:50:22 -05:00
8bb4d4dca3
First pass of the asynchronous block loader.
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Block loads are only triggered on queue empty at this point. Disabled by
default (enable with nt:io=?).
2011-11-18 15:02:59 -05:00
89a581a66f
Added ability to specify arguments in files via -args/--arg_file
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Pushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()
2011-10-24 15:58:34 -04:00
6fa17d86ae
Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator
2011-07-21 00:18:07 -04:00
9992c373be
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.
2011-07-17 20:29:58 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Yossi Farjoun
Mauricio Carneiro
Ami Levy-Moonshine
Eric Banks
kshakir
Matt Hanna
Mark DePristo
David Roazen