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  • 6bd0ec8de4 Proper likelihoods and posterior probability of the joint allele frequency in IndependentAllelesDiploidExactAFCalc Mark DePristo 2012-10-15 20:23:07 -0400
  • d1511e38ad Removing ConstrainedAFCalculationModel; AFCalcPerformanceTest Mark DePristo 2012-10-15 16:06:11 -0400
  • 9fcf71c031 Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component. Added targets to build.xml to effectively 'mvn install' packaged GATK/Queue from ant. TODO: Versions during 'mvn install' are hardcoded at 0.0.1 until a better versioning scheme that works with maven dependencies has been identified. kshakir 2012-10-16 02:21:38 -0400
  • 31be807664 Updating missed integration test. Ryan Poplin 2012-10-15 22:31:52 -0400
  • d27ae67bb6 Updating the multi-step UG integration test. Ryan Poplin 2012-10-15 22:30:01 -0400
  • 6c0e4895f0 added intervals to MuTect in BAM-PP moved intervals from trait to MuTect class Kristian Cibulskis 2012-10-15 22:00:27 -0400
  • 9bb241f06f Merge branch 'develop' of github.com:broadinstitute/cmi-gatk into develop Kristian Cibulskis 2012-10-15 21:59:11 -0400
  • cb33f25bfc Update expected values for HybridSelectionPipelineTest David Roazen 2012-10-15 18:32:15 -0400
  • c4ee31075c Fixed package error and a few deprecated scala warnings. kshakir 2012-10-15 15:29:40 -0400
  • 213cc00abe Refactored argument matching to support other plugins in addition to file lists. Added plugin support for sending Queue status messages. Argument parsing can store subclasses of java.io.File, for example RemoteFile. kshakir 2012-10-15 15:03:33 -0400
  • 4642e4eb66 Merge branch 'unstable' of https://github.com/broadinstitute/cmi-gatk into unstable Mauricio Carneiro 2012-10-15 13:50:03 -0400
  • 69194e5032 Adding intellij example files to the repo Mauricio Carneiro 2012-10-15 13:24:58 -0400
  • ff2307031a Set default parameters for several command line inputs based on refdata content on cloud instances Guillermo del Angel 2012-10-15 12:20:08 -0400
  • b7318f1c96 Bug fixes for temp mutect integration Guillermo del Angel 2012-10-13 22:03:41 -0400
  • c66a4d79ba Further bug fixes to merge cancer/germline fastq-bam pipelines Guillermo del Angel 2012-10-13 11:16:14 -0400
  • 7580548b5f Temp fixes Guillermo del Angel 2012-10-12 16:14:43 -0400
  • 80d92e0c63 Allowing the GATK to have non-required outputs Mauricio Carneiro 2012-10-12 13:50:10 -0400
  • a234bacb02 Making nContigs parameter hidden in ReduceReads Mauricio Carneiro 2012-10-10 15:00:17 -0400
  • d7308646e9 Fix bugs so that we can pass in 2 simultaneous samples in metadata (no co-cleaning yet but at least we don't need to run pipeline twice) to produce 2 bams. Pasted temp mutect so it's also run at the end of the run Guillermo del Angel 2012-10-12 14:39:28 -0400
  • dad7ca281e upgraded mutation caller with VCF output raw indel calls (non filtered,non vcf) Kristian Cibulskis 2012-10-12 14:18:12 -0400
  • 31d6c3538b Some fixes to QC commands in pipeline, and workaround for critical engine bug in GATK that makes it hang when doing small targeted BAM's with a whole exome interval list Guillermo del Angel 2012-10-11 15:08:30 -0400
  • 22b79fb4dd Resolve [DEV-7]: add single-sample VCF calling at end of FASTQ-BAM pipeline. Initial steps of [DEV-4]: queue extensions for Picard QC metrics Guillermo del Angel 2012-10-11 11:09:49 -0400
  • d07df384e7 a) Initial raw version of CMI BAM->VCF pipeline (most likely not working yet, but at least compiles and produces reasonable command lines), b) rename FASTQ->BAM script so name is more descriptive Guillermo del Angel 2012-10-09 11:45:24 -0400
  • 658f355171 initial cancer pipeline with mutations and partial indel support Kristian Cibulskis 2012-10-03 16:25:34 -0400
  • 3e71b238b0 BAM pipeline fixes: a) temp workaround for DEV-9: -nWayOut argument in IndelRealigner is broken, for now things will only really work in single sample mode, b) correct extension of RealignerTargetCreator output, previous extension caused an error Guillermo del Angel 2012-10-04 10:53:13 -0400
  • 91ce0243b0 Minor tweaks to CMIProcessing Pipeline: a) don't hard-code job mem limit to 4 G since it's too much for most AWS instances, leave it instead as input argument, b) minor doc cleanups Guillermo del Angel 2012-10-03 12:05:57 -0400
  • ccd5b22646 Reimplementation of the BAM procesing pipeline using the metadata information file. Mauricio Carneiro 2012-10-02 12:48:55 -0400
  • 6eedd69248 New version of the pipeline starting from an ALIGNED bam going all the way to reducing using n-way out cleaning Mauricio Carneiro 2012-09-26 16:16:53 -0400
  • 6174aa801b Revised implementation of the RAWBAM => BAM pipeline Mauricio Carneiro 2012-09-26 13:37:15 -0400
  • 59bcd0f0d2 First implementation of the CMI data processing pipeline, handling both germline and cancer BAM/FQ => BAM. Mauricio Carneiro 2012-09-25 17:15:42 -0400
  • 322ea1262c First implementation of a generic 'bundled' Data Processing Pipeline for germline and cancer. Mauricio Carneiro 2012-09-25 17:13:50 -0400
  • f1fb51b222 Reverting the DPP to the original version, going to create a new simplified version for CMI in private. Mauricio Carneiro 2012-09-25 12:02:34 -0400
  • 429c96e723 Generic input file name recognition (still need to implement support to FastQ, but it now can at least accept it) Mauricio Carneiro 2012-09-24 17:01:17 -0400
  • 25be94fbb8 Increasing the precision of MathUtils.approximateLog10SumLog10 from 1E-3 to 1E-4. Genotyper integration tests change as a result. Expanding the unit tests of MathUtils.log10sumLog10. Ryan Poplin 2012-10-15 13:24:32 -0400
  • 1977763b08 Set default parameters for several command line inputs based on refdata content on cloud instances Guillermo del Angel 2012-10-15 12:20:08 -0400
  • 0d93effa4d Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ami Levy Moonshine 2012-10-15 11:19:12 -0400
  • d63eaf5b52 add full postQC report option and clean some of the code (it still need more work) Ami Levy Moonshine 2012-10-15 11:17:22 -0400
  • 57e231610b New framework for EXACT calculations, with new 3 new implementations Mark DePristo 2012-10-15 08:32:32 -0400
  • dcf8af42a8 Finalizing IndependentAllelesDiploidExactAFCalc Mark DePristo 2012-10-15 07:40:09 -0400
  • 1ac09ca81e More bugfixes on the way to a final push with new Exact model framework Mark DePristo 2012-10-12 16:16:45 -0400
  • 6b639f51f0 Finalizing new exact model and tests Mark DePristo 2012-10-12 14:06:18 -0400
  • 2d72265f7d AFCalcUnit test a more appropriate name Mark DePristo 2012-10-11 12:56:53 -0400
  • cb857d1640 AFCalcs must be made by factory method now Mark DePristo 2012-10-11 11:05:01 -0400
  • 6bbe750e03 Continuing work on IndependentAllelesDiploidExactAFCalc Mark DePristo 2012-10-10 20:22:23 -0400
  • 176b74095d Intermediate commit on the path to getting a working IndependentAllelesDiploidExact calculation Mark DePristo 2012-10-09 10:35:07 -0400
  • 91aeddeb5a Steps on the way to a fully described and semantically meaningful AFCalcResult Mark DePristo 2012-10-08 19:11:31 -0400
  • 4f1b1c4228 Intermediate commit II on simplifying AFCalcResult Mark DePristo 2012-10-08 12:31:26 -0400
  • 06687bfaf6 Intermediate commit on simplifying AFCalcResult Mark DePristo 2012-10-08 11:04:57 -0400
  • c82aa01e0e Generalize testing infrastructure to allow us to run specific n.samples calculation Mark DePristo 2012-10-07 19:43:55 -0400
  • ec935f76f6 Initial implementation and tests for IndependentAllelesDiploidExactAFCalc Mark DePristo 2012-10-07 18:03:42 -0400
  • 5a4e2a5fa4 Test code to ensure that pNonRef is being computed correctly for at least 1 genotype, bi and tri allelic Mark DePristo 2012-10-05 17:14:55 -0700
  • ee2f12e2ac Simpler naming convention for AlleleFrequencyCalculation => AFCalc Mark DePristo 2012-10-05 15:56:06 -0700
  • cf3f9d6ee8 Reorganize and cleanup AFCalculations Mark DePristo 2012-10-05 15:21:05 -0700
  • 13211231c7 Restructure and cleanup ExactAFCalculations Mark DePristo 2012-10-05 14:49:44 -0700
  • 99ad7b2d71 GeneralPloidyExact should use indel max alt alleles Mark DePristo 2012-10-05 11:49:27 -0700
  • bf276baca0 Don't try to compute full exact model for > 100 samples Mark DePristo 2012-10-05 08:26:42 -0700
  • b924e9ebb4 Add OptimizedDiploidExactAF to PerformanceTesting framework Mark DePristo 2012-10-04 22:10:28 -0700
  • f800f3fb88 Optimized diploid exact AF calculation uses maxACs to stop the calculation by maxAC by allele Mark DePristo 2012-10-04 21:47:28 -0700
  • efad215edb Greedy version of function to compute the max achievable AC for each alt allele Mark DePristo 2012-10-04 20:41:29 -0700
  • 7666a58773 Function to compute the max achievable AC for each alt allele Mark DePristo 2012-10-04 19:38:48 -0700
  • b3cb33a416 simple script to run nano schedule main[] Mark DePristo 2012-10-15 07:52:02 -0400
  • a4767a20be Bug fixes for temp mutect integration Guillermo del Angel 2012-10-13 22:03:41 -0400
  • e3a8ed2151 Further bug fixes to merge cancer/germline fastq-bam pipelines Guillermo del Angel 2012-10-13 11:16:14 -0400
  • b961f78f49 Temp fixes Guillermo del Angel 2012-10-12 16:14:43 -0400
  • 661fa5b98c added support for indel calling (with non-VCF format output) Kristian Cibulskis 2012-10-12 16:02:05 -0400
  • a8efa5451a Protect against bad bases users have screwy data (or try to use zipped references) Eric Banks 2012-10-12 15:05:03 -0400
  • 7e1657d243 Merge branch 'unstable' of github.com:broadinstitute/cmi-gatk into unstable Guillermo del Angel 2012-10-12 14:49:37 -0400
  • 274ac4836f Allowing the GATK to have non-required outputs Mauricio Carneiro 2012-10-12 13:50:10 -0400
  • 05111eeaef Making nContigs parameter hidden in ReduceReads Mauricio Carneiro 2012-10-10 15:00:17 -0400
  • 32e377a0db Fix bugs so that we can pass in 2 simultaneous samples in metadata (no co-cleaning yet but at least we don't need to run pipeline twice) to produce 2 bams. Pasted temp mutect so it's also run at the end of the run Guillermo del Angel 2012-10-12 14:39:28 -0400
  • da1cffbfca Run performance tests in gsa-engineering queue on gsa4 rather than gsa queue David Roazen 2012-10-12 14:18:37 -0400
  • dc03a09722 Merge branch 'develop' into unstable Guillermo del Angel 2012-10-12 14:19:42 -0400
  • c1706ef0ef upgraded mutation caller with VCF output raw indel calls (non filtered,non vcf) Kristian Cibulskis 2012-10-12 14:18:12 -0400
  • 5971006678 Bug fix when running nondiploid mode in UG with EMIT_ALL_SITES: if site was reference-only, QUAL is produced OK but genotypes were being set to no-call because of unnecessary likelihood normalization. May change integration test md5 which I'll fix later today Guillermo del Angel 2012-10-12 12:45:55 -0400
  • 81532a0529 Missing file are user errors. Eric Banks 2012-10-12 09:48:12 -0400
  • fa77a83783 Update the out of space error to include another permutation Eric Banks 2012-10-12 09:38:12 -0400
  • 85525d9e6e Make Geraldine's life easier: from now on we treat problems where a temp file cannot be found when running the GATK with multiple threads as User Errors (since they are 99.9% of the time). This is an extremely large class of errors in Tableau and on the forums. Helpful error message tells users exactly what we tell them on the forums anyways (Geraldine: feel free to edit). Eric Banks 2012-10-12 09:19:50 -0400
  • ad60300bee Catch malformed BAM files at the source since this is the largest class of errors in Tableau. Eric Banks 2012-10-12 09:07:57 -0400
  • 593c8065d9 Fix docs for BadMateFilter Eric Banks 2012-10-12 08:35:45 -0400
  • 6b9987cf1b Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable Christopher Hartl 2012-10-12 00:48:42 -0400
  • c1211ad3a1 Full test suite of LD-corrected GRM calculation. The correctness of this code is now largely verified. Matches GCTA when no correction is used (up to 6 decimal places). Bed reading relies on a particular test directory that is still local. The rest is all generated in unit test fashion. Christopher Hartl 2012-10-12 00:46:02 -0400
  • 3861212dab Fix inefficiency in FilePointer GenomeLoc validation David Roazen 2012-10-11 19:33:37 -0400
  • 47e9d967fe Merging in from cmi-develop branch - staying in this branch for now Guillermo del Angel 2012-10-11 15:35:43 -0400
  • 77949ec740 Some fixes to QC commands in pipeline, and workaround for critical engine bug in GATK that makes it hang when doing small targeted BAM's with a whole exome interval list Guillermo del Angel 2012-10-11 15:08:30 -0400
  • ef3882f439 PhaseByTransmission: small typo /n. variantCallQC_summaryTablesOnly.R: small changes (more to come) /n GeneralCallingPipeline.scala: the new pipeline script. It is not as clean as I want it to be, but it works. I still going to work on it a little bit more. Also, it does not include yet: (1) the RR step (2) need better eval step (3) need to include other targets (currently it eork on the CEU Trio) Ami Levy Moonshine 2012-10-11 14:51:41 -0400
  • af5a6fdace Resolve [DEV-7]: add single-sample VCF calling at end of FASTQ-BAM pipeline. Initial steps of [DEV-4]: queue extensions for Picard QC metrics Guillermo del Angel 2012-10-11 11:09:49 -0400
  • 9b19f5ce99 No longer include stack traces for user exceptions in GATK logs Mark DePristo 2012-10-10 20:41:03 -0400
  • 08b8ce6903 Fixing merge conflicts related to the comment formatting in the BQSR. Ryan Poplin 2012-10-10 16:03:58 -0400
  • 45717349dc Fixing BQSR bug reported on the forum for reads that begin with insertions. Ryan Poplin 2012-10-10 16:01:37 -0400
  • 40a3b5bfe2 Revert "Testing github auto-mirroring attempt #2; please ignore" David Roazen 2012-10-10 15:28:50 -0400
  • fba6a084e4 Testing github auto-mirroring attempt #2; please ignore David Roazen 2012-10-10 15:28:13 -0400
  • 267d1ff59c Revert "Testing the new github auto-mirroring; please ignore" David Roazen 2012-10-10 15:07:48 -0400
  • 66ee3f230f Testing the new github auto-mirroring; please ignore David Roazen 2012-10-10 15:06:50 -0400
  • e9eaa33c0b adding some directories to gitignore Mauricio Carneiro 2012-09-27 11:09:41 -0400
  • 29195cd3aa Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) Mauricio Carneiro 2012-09-27 11:04:56 -0400
  • fdf29503fb removing annoying xml from IDEA configuration Mauricio Carneiro 2012-09-25 17:18:44 -0400
  • e29bcab42e Updating Intellij enviroment and adding Scala Mauricio Carneiro 2012-09-25 10:51:53 -0400
  • f085f5d46a Adding default intellij configuration files Mauricio Carneiro 2012-09-24 16:15:57 -0400
  • 88297606f0 Adding intellij example configuration files Mauricio Carneiro 2012-10-10 13:20:30 -0400
  • c0b7d53170 a) Initial raw version of CMI BAM->VCF pipeline (most likely not working yet, but at least compiles and produces reasonable command lines), b) rename FASTQ->BAM script so name is more descriptive Guillermo del Angel 2012-10-09 11:45:24 -0400