1eab9be35d
Now with accurate javadoc
2011-08-22 17:25:15 -04:00
3612a3501d
info, not warn, about dynamic type determination
2011-08-22 17:24:51 -04:00
f93a554b01
updating exome specific parameters in MDCP
2011-08-21 10:25:36 -04:00
dbff84c54e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-21 10:09:19 -04:00
22ca44c015
Fixed Queue's tagging of RodBindings.
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Fixed argument definition names.
2011-08-21 02:34:20 -04:00
249614e6bb
Record all genes spanning this interval, not just those that start in this interval
2011-08-21 00:23:28 -04:00
9bcceed706
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-20 23:36:33 -04:00
188f28d02b
Increase memory required for merging
2011-08-20 23:35:53 -04:00
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
b008676878
fixing the previous fix
2011-08-20 21:21:55 -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
539e157ecd
Fixing misc parameters in MDCP. The pipeline now does VariantEval of output by default. Fix for NaN vqslod values in VQSR
2011-08-20 11:28:48 -04:00
824583e007
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-20 11:10:15 -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
a96ecbab71
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-19 19:30:05 -04:00
ddb5045e14
Updating the methods development calling pipeline for the new rod binding syntax and the new best practices.
2011-08-19 19:29:51 -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
Mark DePristo
Ryan Poplin
Khalid Shakir
Menachem Fromer
Eric Banks
Guillermo del Angel
Mauricio Carneiro