b0560f9440
Rev. tribble to fix BED codec bug in tribble 51
2012-01-17 16:40:26 -05:00
f2b0575dee
Detect unreasonably large allele strings (>2^16) and throw an error
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-- samtools can emit alleles where the ref is 42M Ns and this caused the GATK (via tribble) to hang in several places.
-- Tribble was updated so we actually could read the line properly (rev. to 51 here).
-- Still the parsing algorithms in the GATK aren't happy with such a long allele. Instead of optimizing the code around an improper use case I put in a limit of 2^16 bp for any allele, and throw a meaningful exception when encountered.
2012-01-17 16:40:26 -05:00
e923a2e512
Revving Picard to incorporate final version of ReadWalker performance improvements.
2012-01-10 12:12:33 -05:00
ea6e718cb8
SnpEff 2.0.5 support. Re-enabled SnpEff in the HybridSelectionPipeline.
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For now, we recommend only running with the GRCh37.64 database.
2012-01-03 15:18:36 -05:00
e6e80e8d3f
Update Picard to fix a bug Mauricio found in Picard where Picard unnecessarily depends on Snappy during some usages of SortingCollection.
2011-12-29 14:35:02 -05:00
b4b7ae1bd9
Revved Picard to incorporate tfennell's AsyncSAMFileWriter.
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Removed DbSnpFileGenerator and related files as they were removed from PPP r2063 by ktibbett.
2011-12-06 10:37:42 -05:00
c9eae32f6e
Revving Tribble to actually close file handles when close() is called.
2011-11-30 22:42:21 -05:00
d7d8b8e380
Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now.
2011-11-28 14:18:28 -05:00
68b2a0968c
Updating the HybridSelectionPipeline for SnpEff 2.0.4 RC3
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This will have to be done again when the 2.0.4 release becomes official,
but it's necessary to do now in order to re-enable the pipeline tests.
2011-11-17 14:46:12 -05:00
d64f8a89a9
Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly.
2011-11-09 15:24:29 -05:00
6297561326
Adding the new jar
2011-11-07 15:08:19 -05:00
aa0c8c3600
Revving Tribble jar to v40. Our last jar was busted.
2011-11-07 11:30:08 -05:00
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
Mark DePristo
Matt Hanna
David Roazen
Khalid Shakir
Eric Banks
Mauricio Carneiro