8aed151a71
Created RevertSam queue class
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Class for the picard tool RevertSam with all the options for queue scripts.
2011-08-22 18:03:39 -04:00
caebc88e9a
Consensus mode and new RodBinding framework.
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The DPP was not using the parameter correctly. It didn't matter for the default option (which is the only one we have been testing) but it would not work for knowns only or smith waterman. It is fixed now.
It now complies with the new rod binding framework.
2011-08-22 18:03:39 -04:00
85c5a6f890
Merge branch 'rodTesting'
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/performance/ProfileRodSystem.java
2011-08-22 17:43:47 -04:00
e728e407d9
First pass Queue script to test progress on ROD refactoring towards Eric+Mark goals
2011-08-22 17:40:35 -04:00
fe7d3ee236
A bit of refinement of the modes
2011-08-22 17:40:02 -04:00
649f134536
Added mode argument that lets you test separately tribble IO and GATK
2011-08-22 17:33:41 -04:00
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
dc42571dd9
Only create the genotype map when necessary
2011-08-22 15:40:36 -04:00
c4c90c8826
Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:
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- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
2011-08-22 15:13:27 -04:00
4ea1ce3c1a
Check for null VCs
2011-08-22 15:11:37 -04:00
2c24b68a96
Working implementation of DecodeLoc for VCF parsing. Makes indexing 3x faster.
2011-08-22 15:11:21 -04:00
518b3dd291
Don't let the genotypes map be null
2011-08-22 15:10:30 -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
Mauricio Carneiro
Mark DePristo
Eric Banks
Khalid Shakir
Ryan Poplin
Menachem Fromer
Guillermo del Angel