9afe6fc7ac
Picard upgrade to 1.55.
2011-10-24 17:02:27 -04:00
84bd355690
Merged bug fix from Stable into Unstable
2011-09-27 14:34:39 -04:00
b090751f62
Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.
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Updates to HybridSelectionPipeline:
- Added annotations back via snpEff
- Minor updates to VQSR paths and lowered memory
2011-09-27 14:33:57 -04:00
34f435565c
Accidentally committed unclean tribble jar to repo
2011-09-21 10:16:17 -04:00
827c942c80
Rev tribble
2011-09-20 14:01:14 -04:00
da9c8ab386
Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly.
2011-09-06 20:39:42 -04:00
0b794b5491
Reving Tribble to 23
2011-09-01 10:43:03 -04:00
dd89755e74
Merged bug fix from Stable into Unstable
2011-08-31 17:28:44 -04:00
65a9159ac6
Point ivy to the maven repo instead of the default ibiblio repo. Drastically
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simplify ivy config by completely cutting out module specifications.
2011-08-31 17:27:25 -04:00
d604019362
Finished my broken tribble code. Updated to rev 22
2011-08-30 16:56:48 -04:00
bdf04b8057
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-30 11:08:23 -04:00
173ca1e215
Reverting tribble temporarily while I fix my subtle problems
2011-08-30 11:08:13 -04:00
2125ba1f23
Merged bug fix from Stable into Unstable
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Conflicts:
private/java/src/org/broadinstitute/sting/pipeline/ReferenceData.java
2011-08-29 19:36:43 -04:00
20ac24464d
Rev'ved picard to read new analysis_files.txt with a blank line after header and no reference sequence.
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Updated error messages and unit tests.
2011-08-29 19:33:04 -04:00
427c643ce7
The missing tribble jar
2011-08-29 18:46:40 -04:00
5defaf5fac
Continuing to improve Tribble
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-- ProfileRodSystem now has a just load index mode, allowing us to optimize the profiler
-- assessFarmNodes R script for making nice plots of performance of jobs on the farm
-- Rev. tribble to use new, optimized index loading (performance win when loading many many indices)
2011-08-29 17:02:57 -04:00
f39d0008bc
Build.xml -- contracts not built by default. Slightly simpler CSS for dl.
2011-08-19 15:07:26 -04:00
f2a05af356
Fixed layout problem with advanced arguments
2011-08-18 21:59:44 -04:00
cca0930517
Better formatting for GATKDocs
2011-08-18 21:24:23 -04:00
ce009bd4a4
Works without related data
2011-08-18 14:05:09 -04:00
a9df365364
GenotypeAndValidate walker updated
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Updated the walker to comply with the new RodBinding system and the new GATKDocs. Will move it to public after writing integration tests.
2011-08-17 21:55:17 -04:00
bd5cdb8a43
The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml
2011-08-11 16:38:29 -04:00
b984b7aa9b
Missing default values are now NA
2011-08-10 22:22:57 -04:00
321afac4e8
Updates to the help layout.
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*New style.css, new template for the walker auto-generated html. Short description is no longer repeated in the long description of the walker.
*Updated DiffObjectsWalker and ContigStatsWalker as "reference" documented walkers.
2011-07-26 19:29:25 -04:00
2039ce6102
Default values now displayed in arguments
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DiffEngine fixed so that newInstance() would work. Pretty quickly encountered a situation where newInstance() failed. Debug output now written when this occurs in the log.
Logger now used instead of standard out, with INFO the default level.
2011-07-24 22:56:55 -04:00
7b84347047
Main index is sorted by the template now.
2011-07-24 18:19:40 -04:00
83996f7951
Enumerated types are working.
2011-07-24 18:14:21 -04:00
3c34e9fa65
Cleanup emuns and tables
2011-07-24 17:45:58 -04:00
c620d96c96
Inline enum documentation is working
2011-07-24 17:22:14 -04:00
793e7d3d1d
Improved header and argument details
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Argument detail structure cleaned up. Only relevant pieces of information are shown now, and in a cleaner layout.
Misc. cleanup in the code.
2011-07-24 16:36:25 -04:00
c6af4efcdc
Implemented see also and version header
2011-07-24 16:10:17 -04:00
b8db0510e0
Sytle sheet and common functions
2011-07-24 15:43:23 -04:00
5e0fe2d0f9
Support for style.css via refactored common.html included in all files
2011-07-24 15:42:39 -04:00
d0ab6bf7a9
Now links to sub and superclass documentation, where possible.
2011-07-24 09:56:17 -04:00
7420ed098e
Semi-working version of extraDocs tag in annotation to refer to one capability being accessible in another
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Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
2011-07-23 22:07:30 -04:00
e262f4e10b
gatkdoc now generalized to use @Annotation. Multiple subsystems now use annotation to receive docs
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Index expanded to use summary() annotation field
UserExceptions, ReadFilters, GATK engine all use the system to generate docs
Doclet expanded to handle lots of new cases
2011-07-23 20:00:35 -04:00
f0be7348be
Generalized handler to allow it to be used with any arbitrary class structure.
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DocumentedGATKFeature now includes a field for the group name.
Build.xml works with public / private now.
2011-07-22 14:07:40 -04:00
453954182e
Generalized the documentation system to use a class-specific annotation and processor.
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Need to generalize and bug fix the system. But at a high level it's working now.
2011-07-22 13:18:33 -04:00
e922ebc29d
Missed this template for walker index.
2011-07-22 09:13:33 -04:00
81d0cab27e
Walker index html now emited.
2011-07-21 16:01:54 -04:00
e892489696
V2 of the document system.
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Now uses GATKDoc class to organize documentation for arguments.
Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html
Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
2011-07-21 15:20:34 -04:00
6fa17d86ae
Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator
2011-07-21 00:18:07 -04:00
baae381acb
Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable"
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This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
2011-07-19 18:38:53 -04:00
9b446020f9
Using picard implementations for accessing aggregation directories.
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Added more utilities to PicardPrivate.
Revved picard.
2011-07-18 21:49:03 -04:00
00b650a35d
Get rid of accidental commit of emacs backup '~' file.
2011-07-17 20:52:46 -04:00
567ed66085
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-17 20:44:43 -04:00
0a0363aef2
Revving Picard to get a parser that works with the latest metrics file formats
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we're starting to see.
2011-07-17 20:43:35 -04:00
35ec82a467
Oops, need this
2011-07-17 13:08:08 -04:00
4db2b13e9e
Rev tribble.
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Just added more documentation for diffEngine and pointer to new wiki:
http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
2011-07-17 13:05:04 -04:00
a5bfcb1ed9
V15 is broken. Going up to v16 in a second.
2011-07-17 10:25:34 -04:00
Matt Hanna
Khalid Shakir
Mark DePristo
Eric Banks
Mauricio Carneiro
David Roazen