a8cbced71b
Bug fix for Ryan: check for no context
2011-08-20 22:49:51 -04:00
0ccd173967
Fixing the recent SelectVariants fix
2011-08-20 21:30:08 -04:00
782453235a
Updated VariantEvalIntegrationTest since there's a new column separating nMixed and nComplex in CountVariants
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Misc updates to WholeGenomeIndelCalling.scala
Bug fix in VariantEval (may be temporary, need more investigation): if -disc option is used in sites-only vcf's then a null pointer exception is produced, caused by recent introduction of -xl_sf options.
2011-08-20 12:24:22 -04:00
0de49f5752
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-20 12:20:38 -04:00
c0227b5cd7
mutt just is broken on gsa2
2011-08-20 10:13:07 -04:00
4939648fd4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-20 08:50:43 -04:00
ff018c7964
Swapped argument order but not MD5 order
2011-08-19 16:55:56 -04:00
8b3cfb2f1c
Final documented version of GATKDoclet and associated classes
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-- Docs on everything.
-- Feature complete. At this point only minor improvements and bugfixes are anticipated
2011-08-19 16:52:17 -04:00
f39d0008bc
Build.xml -- contracts not built by default. Slightly simpler CSS for dl.
2011-08-19 15:07:26 -04:00
b08d63a6b8
Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable
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-- Swapped -o [summary] and -ob [bam] for more standard -o [bam] and -os [summary] arguments.
-- @Advanced arguments
2011-08-19 15:06:37 -04:00
49e831a13b
Should have checked in
2011-08-19 14:35:16 -04:00
e2c066ac1e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-19 14:13:43 -04:00
ee00171b6d
Adding docs to the CGVar codec
2011-08-19 14:13:36 -04:00
01142433d3
Bug fixes to variantCallQC.R so that it doesn't crash if input eval doesn't have indels, misc improvements to WholeGenomeIndelCalling and PostCallingQC scripts
2011-08-19 14:09:08 -04:00
7b5fa4486d
GenotypeAndValidate - Added docs to the @Arguments
2011-08-19 13:35:11 -04:00
a97639b343
Fixing public dependence on private
2011-08-19 13:30:59 -04:00
9f7d4beb89
Merge branch 'help'
2011-08-19 13:14:02 -04:00
4d1fd17a97
GATKDoclet cleanup and documentation
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-- Fixed bug in the way ArgumentCollections were handled that lead to failure in handling the dbsnp argument collection.
2011-08-19 13:13:41 -04:00
67ef18c742
Misc bug fixes to whole genome indel calling script
2011-08-19 11:13:41 -04:00
0f25167efd
minor fix in VariantEval docs
2011-08-19 11:01:04 -04:00
198955f752
GATKDoc descriptions for all standard codecs, or TODO for their owners
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-- Also added vcf.gz support in the VCF codec. This wasn't committed in the last round, because it was missed by the parallel documentation effort.
2011-08-19 09:57:21 -04:00
269ed1206c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-19 09:32:20 -04:00
2bb66e87b3
Several fixes to PostCallingQC.scala: add ability to specify -nt option, update to new rod binding system, defaults to gsa queue.
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Add WholeGenomeIndelCalling.scala script that illustrates best practices for whole genome deep indel calling (e.g. CEU trio)
2011-08-19 09:29:31 -04:00
bc902e8421
GZIP VCF for testing
2011-08-19 09:05:39 -04:00
a5e279d697
Dynamic typing of vcf.gz files
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-- CombineVariantsIntegrationTests now use dynamic typing of vcf.gz files
-- FeatureManagerUnitTests tests for correctness.
2011-08-19 09:05:11 -04:00
40e67cff1b
I like the @Advanced annotation
2011-08-18 22:27:34 -04:00
2457c7b8f5
Merge branch 'master' into help
2011-08-18 22:20:43 -04:00
5fbdf968f7
ArgumentSource no longer comparable. Arguments sorted by GATKDoclet
2011-08-18 22:20:14 -04:00
77fa2c1546
Renaming read filters with a superfluous 'Read' in their names. Kept the ones that made sense to have it (e.g. MalformedReadFilter).
2011-08-18 22:01:33 -04:00
1d3799ddf7
Merge branch 'master' into help
2011-08-18 22:00:29 -04:00
f2a05af356
Fixed layout problem with advanced arguments
2011-08-18 21:59:44 -04:00
d1892cd0d7
Bug fixes
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-- Sorting of ArgumentSources now done in GATKDoclet, not in the ParsingEngine, as the system depends on the LinkedTreeMap
-- Fixed broken exception throwing in the case where a file's type could not be determined
2011-08-18 21:58:36 -04:00
c5efb6f40e
Usability improvements to GATKDocs
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-- ArgumentSources are now sorted by case insensitive names, so arguments are shown in alphabetical order (Ryan)
-- @Advanced annotation can be used to indicate that an argument is an advanced option and should be visually deemphasized in the GATKs. There's now an advanced section. Mauricio or Ryan -- could you figure out how to make this section less prominent in the style.css?
2011-08-18 21:39:11 -04:00
cca0930517
Better formatting for GATKDocs
2011-08-18 21:24:23 -04:00
d94da0b1cf
Moved CG and SOAP codecs to private
2011-08-18 21:20:26 -04:00
f7414e39bc
Improvements to GATKDocs
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-- Allowed values for RodBinding<T> are displayed in the GATKDocs
-- Longest name up to 30 characters is chosen for main argument list (suggested by Ryan/Mauricio)
-- Features are listed in alphabetical order
-- Moved useful getParameterizedType() function to JVMUtils
-- Tests of these features in the Documentation Test
2011-08-18 21:20:09 -04:00
09d099cada
Added GATKDocs to the UnifiedGenotyper.
2011-08-18 20:57:02 -04:00
626cbf9411
Bug fixes and cleanups for IndelStatistics
2011-08-18 16:28:40 -04:00
58560a6d50
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 16:17:52 -04:00
3dfb60a46e
Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases.
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VariantEval module CountVariants is corrected and an additional column is added so that we log mixed events and complex indels separately (before they were being conflated).
VariantEval module IndelStatistics is considerably simplified as the sample stratification was wrong and redundant, now it should work with the VE-generic Sample stratification. Several columns are renamed or removed since they're not really useful
2011-08-18 16:17:38 -04:00
6b256a8ac5
Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git
2011-08-18 15:29:24 -04:00
6ee54cce32
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 15:29:13 -04:00
a8935c99fc
dding docs for DepthOfCoverage and ValidationAmplicons
2011-08-18 15:28:35 -04:00
f2f51e35e3
Merge branch 'master' into help
2011-08-18 14:05:33 -04:00
ce009bd4a4
Works without related data
2011-08-18 14:05:09 -04:00
faa3f8b6f6
Only concrete classes are now documented
2011-08-18 14:04:47 -04:00
7c4ce6d969
Added GATKDocs for the VQSR walkers.
2011-08-18 14:00:39 -04:00
5772766dd5
Improvements to GATKDocs
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-- Now supports a static list of root classes / interfaces that should receive docs. A complementary approach to documenting features to the DocumentedGATKFeature annotation
-- Tribble codecs are now documented!
-- No longer displayed sub and super classes
2011-08-18 14:00:09 -04:00
10d8033bcf
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 12:58:16 -04:00
8b37a2d976
Could not get Khalid's DoC hack (for me) to play nicely with relative paths, although this somehow used to work. So, I made sure not to include paths in scattered commands. This would be a lot easier if DoC worked with Queue's Input/Output system. But, my long-term plan is still to write a new simpler DoC walker that will have less functionality but conform to the Queue model...
2011-08-18 12:39:52 -04:00
Eric Banks
Guillermo del Angel
Mark DePristo
Mauricio Carneiro
Ryan Poplin
Chris Hartl
Menachem Fromer