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  • 649f134536 Added mode argument that lets you test separately tribble IO and GATK Mark DePristo 2011-08-22 17:33:41 -0400
  • 1eab9be35d Now with accurate javadoc Mark DePristo 2011-08-22 17:25:15 -0400
  • 3612a3501d info, not warn, about dynamic type determination Mark DePristo 2011-08-22 17:24:51 -0400
  • 9fb208c8f0 First Working Implementation Roger Zurawicki 2011-08-22 16:46:24 -0400
  • dc42571dd9 Only create the genotype map when necessary Eric Banks 2011-08-22 15:40:36 -0400
  • c4c90c8826 Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline: - 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. Khalid Shakir 2011-08-22 15:12:55 -0400
  • 4ea1ce3c1a Check for null VCs Eric Banks 2011-08-22 15:11:37 -0400
  • 2c24b68a96 Working implementation of DecodeLoc for VCF parsing. Makes indexing 3x faster. Eric Banks 2011-08-22 15:11:21 -0400
  • 518b3dd291 Don't let the genotypes map be null Eric Banks 2011-08-22 15:10:30 -0400
  • 17ce38dd63 Partially Fixed bug where the 'H' operator was counted extra times Roger Zurawicki 2011-08-22 13:56:12 -0400
  • 600456f880 Merging initial minor fixes / modifications to the assembler Ryan Poplin 2011-08-22 09:22:44 -0400
  • a4cf34ef38 Initial commit of the haplotype caller Ryan Poplin 2011-08-22 08:52:31 -0400
  • d111903322 Added trimmedLeft/Right field, and output clones SAMRecord Roger Zurawicki 2011-08-21 17:56:50 -0400
  • f93a554b01 updating exome specific parameters in MDCP Ryan Poplin 2011-08-21 10:25:36 -0400
  • dbff84c54e Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-21 10:09:19 -0400
  • 22ca44c015 Fixed Queue's tagging of RodBindings. Fixed argument definition names. Khalid Shakir 2011-08-21 02:34:20 -0400
  • 249614e6bb Record all genes spanning this interval, not just those that start in this interval Menachem Fromer 2011-08-21 00:23:28 -0400
  • 9bcceed706 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2011-08-20 23:36:33 -0400
  • 188f28d02b Increase memory required for merging Menachem Fromer 2011-08-20 23:35:53 -0400
  • a8cbced71b Bug fix for Ryan: check for no context Eric Banks 2011-08-20 22:49:51 -0400
  • 0ccd173967 Fixing the recent SelectVariants fix Eric Banks 2011-08-20 21:30:08 -0400
  • b008676878 fixing the previous fix Ryan Poplin 2011-08-20 21:21:55 -0400
  • 782453235a Updated VariantEvalIntegrationTest since there's a new column separating nMixed and nComplex in CountVariants 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. Guillermo del Angel 2011-08-20 12:24:22 -0400
  • 0de49f5752 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-20 12:20:38 -0400
  • 539e157ecd Fixing misc parameters in MDCP. The pipeline now does VariantEval of output by default. Fix for NaN vqslod values in VQSR Ryan Poplin 2011-08-20 11:28:48 -0400
  • 824583e007 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-20 11:10:15 -0400
  • c0227b5cd7 mutt just is broken on gsa2 Mark DePristo 2011-08-20 10:13:07 -0400
  • 4939648fd4 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-20 08:50:43 -0400
  • a96ecbab71 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-19 19:30:05 -0400
  • ddb5045e14 Updating the methods development calling pipeline for the new rod binding syntax and the new best practices. Ryan Poplin 2011-08-19 19:29:51 -0400
  • ff018c7964 Swapped argument order but not MD5 order Mark DePristo 2011-08-19 16:55:56 -0400
  • 8b3cfb2f1c Final documented version of GATKDoclet and associated classes Mark DePristo 2011-08-19 16:52:17 -0400
  • f39d0008bc Build.xml -- contracts not built by default. Slightly simpler CSS for dl. Mark DePristo 2011-08-19 15:07:26 -0400
  • b08d63a6b8 Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable Mark DePristo 2011-08-19 15:06:37 -0400
  • 49e831a13b Should have checked in Mark DePristo 2011-08-19 14:35:16 -0400
  • e2c066ac1e Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-19 14:13:43 -0400
  • ee00171b6d Adding docs to the CGVar codec Eric Banks 2011-08-19 14:13:36 -0400
  • 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 Guillermo del Angel 2011-08-19 14:09:08 -0400
  • aa4e8f35a7 Simplified read in map() Mauricio Carneiro 2011-08-19 14:03:04 -0400
  • 7b5fa4486d GenotypeAndValidate - Added docs to the @Arguments Mauricio Carneiro 2011-08-19 13:34:21 -0400
  • a97639b343 Fixing public dependence on private Mark DePristo 2011-08-19 13:30:59 -0400
  • 9f7d4beb89 Merge branch 'help' Mark DePristo 2011-08-19 13:14:02 -0400
  • 4d1fd17a97 GATKDoclet cleanup and documentation Mark DePristo 2011-08-19 13:13:41 -0400
  • 67ef18c742 Misc bug fixes to whole genome indel calling script Guillermo del Angel 2011-08-19 11:13:41 -0400
  • 0f25167efd minor fix in VariantEval docs Ryan Poplin 2011-08-19 11:01:04 -0400
  • 198955f752 GATKDoc descriptions for all standard codecs, or TODO for their owners Mark DePristo 2011-08-19 09:57:21 -0400
  • 269ed1206c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-19 09:32:20 -0400
  • 2bb66e87b3 Several fixes to PostCallingQC.scala: add ability to specify -nt option, update to new rod binding system, defaults to gsa queue. Add WholeGenomeIndelCalling.scala script that illustrates best practices for whole genome deep indel calling (e.g. CEU trio) Guillermo del Angel 2011-08-19 09:29:31 -0400
  • bc902e8421 GZIP VCF for testing Mark DePristo 2011-08-19 09:05:39 -0400
  • a5e279d697 Dynamic typing of vcf.gz files Mark DePristo 2011-08-19 09:05:11 -0400
  • 40e67cff1b I like the @Advanced annotation Eric Banks 2011-08-18 22:27:34 -0400
  • 2457c7b8f5 Merge branch 'master' into help Mark DePristo 2011-08-18 22:20:43 -0400
  • 5fbdf968f7 ArgumentSource no longer comparable. Arguments sorted by GATKDoclet Mark DePristo 2011-08-18 22:20:14 -0400
  • 77fa2c1546 Renaming read filters with a superfluous 'Read' in their names. Kept the ones that made sense to have it (e.g. MalformedReadFilter). Eric Banks 2011-08-18 22:01:33 -0400
  • 1d3799ddf7 Merge branch 'master' into help Mark DePristo 2011-08-18 22:00:29 -0400
  • f2a05af356 Fixed layout problem with advanced arguments Mark DePristo 2011-08-18 21:59:44 -0400
  • d1892cd0d7 Bug fixes Mark DePristo 2011-08-18 21:58:36 -0400
  • c5efb6f40e Usability improvements to GATKDocs Mark DePristo 2011-08-18 21:39:11 -0400
  • cca0930517 Better formatting for GATKDocs Mark DePristo 2011-08-18 21:24:23 -0400
  • d94da0b1cf Moved CG and SOAP codecs to private Mark DePristo 2011-08-18 21:20:26 -0400
  • f7414e39bc Improvements to GATKDocs Mark DePristo 2011-08-18 21:20:09 -0400
  • 09d099cada Added GATKDocs to the UnifiedGenotyper. Ryan Poplin 2011-08-18 20:57:02 -0400
  • 6ef01e40b8 Complete rewrite of Hard Clipping (ReadClipper) Mauricio Carneiro 2011-08-18 18:35:45 -0400
  • 626cbf9411 Bug fixes and cleanups for IndelStatistics Guillermo del Angel 2011-08-18 16:28:40 -0400
  • 58560a6d50 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-18 16:17:52 -0400
  • 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. 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 Guillermo del Angel 2011-08-18 16:17:38 -0400
  • 6b256a8ac5 Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git Chris Hartl 2011-08-18 15:29:24 -0400
  • 6ee54cce32 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-08-18 15:29:13 -0400
  • a8935c99fc dding docs for DepthOfCoverage and ValidationAmplicons Chris Hartl 2011-08-18 15:28:35 -0400
  • f2f51e35e3 Merge branch 'master' into help Mark DePristo 2011-08-18 14:05:33 -0400
  • ce009bd4a4 Works without related data Mark DePristo 2011-08-18 14:05:09 -0400
  • faa3f8b6f6 Only concrete classes are now documented Mark DePristo 2011-08-18 14:04:47 -0400
  • 7c4ce6d969 Added GATKDocs for the VQSR walkers. Ryan Poplin 2011-08-18 14:00:39 -0400
  • 5772766dd5 Improvements to GATKDocs Mark DePristo 2011-08-18 14:00:09 -0400
  • 10d8033bcf Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-08-18 12:58:16 -0400
  • 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... Menachem Fromer 2011-08-18 12:39:52 -0400
  • e03db30ca0 New uses DocumentedGATKFeatureObject instead of annotation directly Mark DePristo 2011-08-18 12:31:04 -0400
  • 3a6a206940 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-08-18 12:23:32 -0400
  • ff45fc9d5a Output proper quality score string, slightly better insert size metrics Chris Hartl 2011-08-18 11:58:34 -0400
  • d4511807ed Merge branch 'master' into help Mark DePristo 2011-08-18 11:53:37 -0400
  • c787fd0b70 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-18 11:52:45 -0400
  • c797616c65 If you have one sample in your BAM, getToolkit().getSamples().size() == 2 Mark DePristo 2011-08-18 11:51:53 -0400
  • 690f691ea9 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2011-08-18 11:46:08 -0400
  • cbec69a130 Merge branch 'master' into help Mark DePristo 2011-08-18 11:33:27 -0400
  • aa21fc7c9c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-18 11:30:59 -0400
  • f5d7cabb20 Fix for reintroducing an already solved problem. Mark DePristo 2011-08-18 11:20:12 -0400
  • a45498150a Remove non-ascii char Eric Banks 2011-08-18 11:18:29 -0400
  • c08a9964d4 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-18 10:58:04 -0400
  • bb79d3edae Added GATKDocs for the BQSR walkers. Ryan Poplin 2011-08-18 10:57:48 -0400
  • 47bbddb724 Now provides type-specific user feedback Mark DePristo 2011-08-18 10:47:16 -0400
  • ecfabd134f Created a non destructive trim method for variable sites Roger Zurawicki 2011-08-16 13:35:29 -0400
  • 2d41ba15a4 Vastly better Tribble help message Mark DePristo 2011-08-18 10:31:32 -0400
  • c2287c93d7 Cleanup of codec locations. No more dbSNPHelper Mark DePristo 2011-08-18 10:02:46 -0400
  • 9c17d54cb6 getFeatureClass() now returns Class<T> not Class to avoid yesterday's runtime error Mark DePristo 2011-08-18 09:39:20 -0400
  • c30e1db744 Better location for help utils Mark DePristo 2011-08-18 09:38:51 -0400
  • 4da42d9f39 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-18 09:32:57 -0400
  • de35bb2e4d Update hard-coded path of CNV read-depth merging script. The design of this pipeline needs to be corrected in the next few months... Menachem Fromer 2011-08-18 00:10:12 -0400
  • c91a442be1 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-17 22:40:16 -0400
  • b75a1807e3 Adding integration test to cover sample exclusion Eric Banks 2011-08-17 22:40:09 -0400
  • a7b70e6bb4 Adding feature for Khalid: ability to exclude particular samples. Eric Banks 2011-08-17 22:28:22 -0400