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  • d1b2b4ece9 Simple R script to analyse node performance Mark DePristo 2011-08-28 16:40:38 -0400
  • 796ba34f6d Simple script that can be used to access farm node performance Mark DePristo 2011-08-28 15:09:50 -0400
  • 7542d29507 Oops, enabling default displays again Mark DePristo 2011-08-28 12:07:38 -0400
  • 84704aaee3 Support for exechosts. Only displays by default in the gantt chart as jobname @ exechosts. Mark DePristo 2011-08-28 12:06:41 -0400
  • b38de1fa35 Now captures the exechost in the job report Mark DePristo 2011-08-28 12:05:56 -0400
  • 7bf006278d Moved ResolveHostname to general utils as a static function Mark DePristo 2011-08-28 12:04:16 -0400
  • 77426d0fe1 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-28 09:31:15 -0400
  • 32e74affe1 Sliding Window refactor to account for indels Mauricio Carneiro 2011-08-27 14:23:15 -0400
  • ccec0b4d73 AnalyzeCovariates uses the general RScript system now Mark DePristo 2011-08-27 12:54:13 -0400
  • 810a71c631 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-27 10:50:15 -0400
  • 1ceb020fae UnitTests for RScript Mark DePristo 2011-08-27 10:50:05 -0400
  • ede4b0a116 Now includes the standard deviation in the average parameter results Mark DePristo 2011-08-27 09:57:10 -0400
  • 50908fe285 Enable conditional inclusion of documentation for hidden features in GATKDocs. David Roazen 2011-08-27 03:17:46 -0400
  • ccfed5d64d Enable Contracts for Java by default for test targets. David Roazen 2011-08-27 02:32:47 -0400
  • 732f1f12b7 Refactoring Sliding window Mauricio Carneiro 2011-08-26 18:25:49 -0400
  • beb947d3cc Standalone program to create an XML index of the GSA pipeline directory suitable for loading in IGV. David Roazen 2011-08-23 10:39:15 -0400
  • 6c8cafba63 CountsWithBases now handles indels Mauricio Carneiro 2011-08-26 14:41:16 -0400
  • dd2cf7d81e Evaluating the likelihood of a haplotype should only use the passing reads Ryan Poplin 2011-08-26 14:36:28 -0400
  • 5a6ae954bf Added VCF streaming to tribbleVsGATK Mark DePristo 2011-08-26 14:04:48 -0400
  • bd92a1b220 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-08-26 13:24:26 -0400
  • e37a638e09 Fix for disallowed characters in GATKReportTable Mark DePristo 2011-08-26 13:24:06 -0400
  • 6e66f1c243 Removing code that cleans up the assembly graph for purposes of display. There seems to be bugs Ryan Poplin 2011-08-26 12:36:12 -0400
  • 8f150c6764 Assembly debug mode now uses smith-waterman to locally align all haplotypes and outputs to a bam file instead of first writing a fasta file and using bwa-sw outside of the GATK. Ryan Poplin 2011-08-26 10:43:40 -0400
  • 8f90a22555 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-26 10:16:56 -0400
  • 0cb1605df0 Clean documentation for JobRunInfo Mark DePristo 2011-08-26 09:22:58 -0400
  • 415d5d5301 LSF long times are in seconds, convert to milliseconds to meet standard Mark DePristo 2011-08-26 09:18:28 -0400
  • c11ddf3da3 Enchancements to queueJobReport Mark DePristo 2011-08-26 09:17:09 -0400
  • c0503283df Spelling fix requires md5 updates Mark DePristo 2011-08-26 07:40:44 -0400
  • eef1ac415a Merge branch 'master' into rodTesting Mark DePristo 2011-08-26 00:35:41 -0400
  • 6bd3959ff2 Now shows job scheduling over time Mark DePristo 2011-08-26 00:19:50 -0400
  • 34fb6ef798 SitesVsGenotypes should only be on chr1 Mark DePristo 2011-08-26 00:18:09 -0400
  • c0e55c5ca4 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-25 22:42:27 -0400
  • 9b7512fd94 Just because there's a ref base doesn't mean the VC needs to be padded Eric Banks 2011-08-25 22:42:14 -0400
  • 6d8851eb63 Added option to control memory usage of DoC merging step Menachem Fromer 2011-08-25 22:12:54 -0400
  • 03a655023c Must explicitly enable multithreaded tests Mark DePristo 2011-08-25 19:41:08 -0400
  • 1a50a251d8 Draft version of report Mark DePristo 2011-08-25 17:03:50 -0400
  • e03dfdb0ab Automatic iteration field addition works properly. Mark DePristo 2011-08-25 16:59:02 -0400
  • e01273ca7c Queue now writes out queueJobReport.pdf Mark DePristo 2011-08-25 16:57:11 -0400
  • e132c97098 *Glitch at Low Coverage Gap Roger Zurawicki 2011-08-25 16:56:36 -0400
  • 09a729da3a Removing incorrect comment Eric Banks 2011-08-25 15:42:52 -0400
  • 3eed5af2f7 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-08-25 15:37:35 -0400
  • 8bbef79fc2 Create clipped alleles during allele parsing instead of creating a full VC, clipping alleles, and regenerating the VC from scratch. Eric Banks 2011-08-25 15:37:26 -0400
  • c34b4b20aa Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-25 14:58:15 -0400
  • 6347317ba8 Too fast to commit last time Guillermo del Angel 2011-08-25 14:58:10 -0400
  • 0f4be2c4a4 Argument to disable queueJobReport entirely Mark DePristo 2011-08-25 13:32:03 -0400
  • 999dff1252 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-25 13:28:23 -0400
  • 1bf0fcd7a4 Obvious bug fix in HSP script: not enough to fix test yet, though Guillermo del Angel 2011-08-25 13:27:55 -0400
  • d81122cf5f Fixed up so that all modes can go through multiple iterations Eric Banks 2011-08-25 13:22:39 -0400
  • d65faf509c Default output name for Queue JobReport is queue_jobreport.gatkreport.txt Mark DePristo 2011-08-25 13:15:20 -0400
  • a7d6946b22 Refactored QJobReport and QFunction, which is now automatically tracked Mark DePristo 2011-08-25 13:13:55 -0400
  • 08f6c3eea9 companion gantt charts for Q runtimes Mark DePristo 2011-08-25 12:59:59 -0400
  • e5ca61e371 Bug fix for multiallelic events in haplotype caller Ryan Poplin 2011-08-25 11:09:39 -0400
  • 5e0660e27d Adding debug option to output all possible haplotypes in fasta format for use with bwa Ryan Poplin 2011-08-25 10:31:10 -0400
  • 16caca0822 BLASR BAMs and new BWA parameters Mauricio Carneiro 2011-08-24 17:02:44 -0400
  • e3f5d7067a Added ReorderSam queue binding Mauricio Carneiro 2011-08-24 14:07:54 -0400
  • 08fb21f127 Removing hostname Mark DePristo 2011-08-24 16:45:50 -0400
  • d50474f14c Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-08-24 16:06:36 -0400
  • dc8398e165 fixing bai output for indel cleaning. Mauricio Carneiro 2011-08-24 15:58:34 -0400
  • da5e6b52e7 Refactoring the smith-waterman and genotyping-related pieces into their own engine Ryan Poplin 2011-08-24 15:54:17 -0400
  • 06e30a81d1 Fixes throughout for getting job information Mark DePristo 2011-08-24 15:30:09 -0400
  • 29c7b10f7b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-24 15:18:58 -0400
  • e5008aba00 Output the top two haplotypes as a variant call by running smith-waterman alignment against the reference and calling any difference as variation. This is the first verion that runs end-to-end by taking in reads as bam file and writing out variant calls in VCF. Ryan Poplin 2011-08-24 15:18:44 -0400
  • 4918519a58 No more NPE in getRuntime() when you cntr-c out of Queue Mark DePristo 2011-08-24 14:14:01 -0400
  • 16d8360592 QJobReport is now the official capability name Mark DePristo 2011-08-24 13:59:14 -0400
  • d047c19ad1 Writes output to file Mark DePristo 2011-08-24 13:52:05 -0400
  • 61f5968807 Change indel/snp selection to new arguments Guillermo del Angel 2011-08-24 13:42:23 -0400
  • 3ae68e2397 JobLogging trait now writes out GATKReport log of jobs Mark DePristo 2011-08-24 13:36:39 -0400
  • e618cb1e79 a) Renamed/expanded SelectVariants arguments that choose particular kinds of variants and particular allelic types, now instead of -Indels or -SNPs we can specify for example -selectType [MIXED|INDEL|SNP|MNP|SYMBOLIC]. To select biallelic, multiallelic variants, use -restrictAllelesTo [BIALLELIC|MULTIALLELIC]. Corresponding gatkdocs changes. b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk). c) Added integrationtest for new SelectVariants commands Guillermo del Angel 2011-08-24 12:25:50 -0400
  • cd12f7f286 Fixed list dependency Mauricio Carneiro 2011-08-24 11:10:40 -0400
  • 219252a566 Adapting to the new RodBinding framework Mauricio Carneiro 2011-08-23 15:38:19 -0400
  • 28ee6dac41 Fixed spelling mistake Mark DePristo 2011-08-24 10:14:45 -0400
  • f37875600a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-24 09:02:44 -0400
  • 1ecbf05aae Avoid segfaults due to out of date and possibly abandonded LSF DRMAA implementation when use'ing LSF instead of .combined_LSF_SGE Khalid Shakir 2011-08-23 23:49:36 -0400
  • b8bc03bb42 JobRunInfo improvements Mark DePristo 2011-08-23 17:11:22 -0400
  • 569e1a1089 Walker.isDone() aborts execution early Mark DePristo 2011-08-23 16:53:06 -0400
  • 31ec6e316c First implementation of JobRunInfo Mark DePristo 2011-08-23 16:51:54 -0400
  • 7d653c48b1 Consensus Reads call close() when crossing a gap Roger Zurawicki 2011-08-23 16:07:10 -0400
  • 08e5503a60 Likelihood engine now gives non-zero likelihoods. Using HMM function that can handle context specific gap open and gap continuation penalties Ryan Poplin 2011-08-23 13:43:43 -0400
  • a1a1fac9e4 Likelihood engine now gives non-zero likelihoods. Using HMM function that can handle context specific gap open and gap continuation penalties Ryan Poplin 2011-08-23 13:43:07 -0400
  • 3c37d841db Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-08-23 13:05:12 -0400
  • 6e2552a9ef Merge fix Guillermo del Angel 2011-08-23 12:40:43 -0400
  • 8b7a0b3b62 Two new arguments to SelectVariants to exclude either multiallelic or biallelic sites from input vcf Guillermo del Angel 2011-08-23 12:40:01 -0400
  • ac36271457 Fixed extra reads showing up in Variable Sites Roger Zurawicki 2011-08-23 11:26:00 -0400
  • 6d6feb5540 Better error message when you cannot determine a ROD type because the file doesn't exist or cannot be read Mark DePristo 2011-08-23 10:56:37 -0400
  • bcc0cae89e Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-23 10:51:24 -0400
  • bd26de9741 Resurrect IndelCountCovariates walker, update to new rod system. IndelCountCovariate (singular) seems broken, not to be used for now (but it's not very useful anyway) Guillermo del Angel 2011-08-23 10:50:55 -0400
  • a9ba945595 onExecutionDone(jobs, successFlag) added to QScript. Mark DePristo 2011-08-23 10:09:51 -0400
  • 9597d6edad Commented out debug info Roger Zurawicki 2011-08-22 17:05:38 -0400
  • feeab6075f Merging ReduceReads development with unstable repo Mauricio Carneiro 2011-08-22 23:03:03 -0400
  • af4db34407 Apparently git can't deal with renaming a file that only changes capitalization? Guillermo del Angel 2011-08-22 22:00:04 -0400
  • ee68713267 Further Bug fixes to CountVariants: stratifications were wrong in case genotypes had no-calls, for example if we stratified by sample and a sample had a no-call, this no-call was considered a true variant and counts were incorrectly increased Guillermo del Angel 2011-08-22 20:42:47 -0400
  • c270384b2e Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-08-22 20:39:32 -0400
  • 8ae24912f4 a) Misc fixes in Phase1 indel vqsr script, b) More R-friendly VariantsToTable printing of AC in case of multiple alt alleles c) Rename FixPLOrderingWalker to FixGenotypesWalker and rewrote: no longer need older code, replaced with code to replace genotypes with all-zero PL's with a no-call. Guillermo del Angel 2011-08-22 20:39:06 -0400
  • 136f0eb685 Creating sample-bam list instead of joining Mauricio Carneiro 2011-08-22 18:00:44 -0400
  • 04d8bcaf19 Fixed bai removal on picard tools Mauricio Carneiro 2011-08-22 14:42:29 -0400
  • 8aed151a71 Created RevertSam queue class Mauricio Carneiro 2011-08-22 14:23:39 -0400
  • caebc88e9a Consensus mode and new RodBinding framework. Mauricio Carneiro 2011-08-22 14:05:13 -0400
  • 85c5a6f890 Merge branch 'rodTesting' Mark DePristo 2011-08-22 17:43:47 -0400
  • e728e407d9 First pass Queue script to test progress on ROD refactoring towards Eric+Mark goals Mark DePristo 2011-08-22 17:40:35 -0400
  • fe7d3ee236 A bit of refinement of the modes Mark DePristo 2011-08-22 17:40:02 -0400