zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Commit Graph

  • 9c384b4813 Near final version of 1000G Phase I table script Mark DePristo 2012-03-27 11:52:07 -0400
  • 913c8b231f Fix ErrorRatePerCycle to overload equals and hashcode Mark DePristo 2012-03-27 10:34:56 -0400
  • c07a577ba3 Significant restructuring of the Exact model, as discussed within the dev group last week. There is no more marginalizing over alternate alleles, and we now keep track of the MLE and MAP. Important notes: 1) integration tests change because the previous marginalization wasn't done correctly (as pointed out by Guillermo) and our confidences were too high for many multi-allelic sites; 2) there is a major TO-DO item that needs to be discussed within the dev group (so they should expect a follow up email); 3) this code is still in flux as I am awaiting feedback from Ryan now on its performance with the Haplotype Caller (the good news, Ryan, is that we recover that site that we were losing previously). Eric Banks 2012-03-27 00:27:44 -0500
  • e8bb8ade1a Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-03-26 16:42:03 -0400
  • 1a2a4848e8 Added integration test for ValidationSiteSelector, correct MD5's Guillermo del Angel 2012-03-26 16:39:55 -0400
  • 34ea443cdb Better algorithm for choosing which indel alleles are present in samples Mark DePristo 2012-03-26 16:28:02 -0400
  • 11b6fd990a GATKReportColumn optimizations Mark DePristo 2012-03-26 10:39:45 -0400
  • a0dcac9ec6 Indel length distributions are now boxplots Mark DePristo 2012-03-26 10:38:46 -0400
  • 6be5e82860 VariantEval scalability optimizations Mark DePristo 2012-03-26 07:42:15 -0400
  • 1c424c0daf Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-03-26 15:15:50 -0400
  • 8f0828daa6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-03-26 11:32:58 -0400
  • 019145175b Major optimizations to graph construction through better use of built in graph.containsVertex and vertex.equals methods. Minor optimizations to MathUtils.approximateLog10SumLog10 method Ryan Poplin 2012-03-26 11:32:44 -0400
  • dcc354c38e Continuing to improve stack trace formatting. Now includes error message as well Mark DePristo 2012-03-26 08:17:27 -0400
  • 1fa66f76c9 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-03-25 23:04:47 -0400
  • 3bf650ec18 bug fix for concurrent modification exception when path cache size was exceeded. Ryan Poplin 2012-03-25 20:44:45 -0400
  • ce617b2dfc Bug fix to previous UnifiedGenotyperEngine refactoring, removed debug code Guillermo del Angel 2012-03-25 10:20:21 -0400
  • db54c2625f Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-03-25 09:53:35 -0400
  • c4f0d7eb73 Added mode to call SNPs and indels separately. Added functional annotation step back in. Eric Banks 2012-03-25 09:06:28 -0400
  • deb4586559 Next intermediate commit for new pool caller structure: a) Bug fixes in pool GL computation. Now, correct GL's are returned per each pool to the UG engine. Work still needs to be done in redoing interface with exact model. b) Added unit tests for new MathUtils dot product and logDotProduct functions. c) Refactorings of UnifiedGentotyperEngine since N (size of prior/posterior arrays) is no longer necessarily nSamples+1 but, in general, nSamplesPerPool*nPools+1 Guillermo del Angel 2012-03-24 21:49:43 -0400
  • 76d88a2577 Scale the pruning of the assembly graph with the approximate per-sample coverage of the region. Get rid of the PriorityQueue in the assembly graph traversal because it is too slow. Ryan Poplin 2012-03-24 11:57:40 -0400
  • b063bcd38d Removing update0 support in VariantEval Mark DePristo 2012-03-23 21:02:21 -0400
  • 5e93dc690d Bug fix for when a node has an edge pointing to itself and was trying to merge with itself. Bug fix for edge class not using the vertex object equals function. Ryan Poplin 2012-03-23 16:40:03 -0400
  • 0509d316d9 More information in the recalibration report Mauricio Carneiro 2012-03-23 16:15:19 -0400
  • 9f74969e3a BQSR with GATKReport implementation Mauricio Carneiro 2012-03-19 18:00:30 -0400
  • f421062b55 Updated read group covariate to use sample.lane instead of the id Mauricio Carneiro 2012-03-19 16:04:45 -0400
  • 539da9e3e1 Fixing GATKReport exception handling when loading a report Mauricio Carneiro 2012-03-23 13:54:46 -0400
  • 4a54a4b11c Bugfixes to variantCallQC.R; improved visual style Mark DePristo 2012-03-23 15:03:45 -0400
  • 2511839068 Merged bug fix from Stable into Unstable Eric Banks 2012-03-23 13:51:33 -0400
  • d3f2bc4361 Pre-allocate 10 alt alleles worth of PLs in the cache for efficiency. This effectively means that we never need to re-allocate the cache in the future because we can't ever really handle that many alt alleles. Eric Banks 2012-03-23 13:51:00 -0400
  • e4ec90cfce Merged bug fix from Stable into Unstable Mark DePristo 2012-03-23 11:27:34 -0400
  • ff26f2bf68 HierarchicalMicroScheduler no longer attempts to wrap exceptions Mark DePristo 2012-03-23 11:27:10 -0400
  • fdd37e0798 Strings are way too slow. Now uses ArrayUtils to append arrays of bytes (paths) together. Ryan Poplin 2012-03-23 11:16:03 -0400
  • 9d22471b79 Merged bug fix from Stable into Unstable Ryan Poplin 2012-03-23 10:48:34 -0400
  • ab288354e9 Better error message for malformed input recal file. Ryan Poplin 2012-03-23 10:47:01 -0400
  • a42fd5e935 More informative stack trace formatting for analyzeRunReports.py Mark DePristo 2012-03-23 09:03:49 -0400
  • fee8d86f63 VariantEval optimization Mark DePristo 2012-03-22 22:13:24 -0400
  • a0602e534c PostCallingQC and variantCallQC.R vastly improved Mark DePristo 2012-03-22 21:21:13 -0400
  • 6df96644d9 Unified, standard IndelSummary metrics for VariantEval Mark DePristo 2012-03-22 21:18:38 -0400
  • bcf80cc7b3 Cleanup in VariantEval. Example of molten VariantEval output Mark DePristo 2012-03-22 21:14:44 -0400
  • e4d49357ce Further cleanup of R Mark DePristo 2012-03-22 21:08:08 -0400
  • 503e2ea29e Cleanup R directory Mark DePristo 2012-03-22 21:06:10 -0400
  • 5725f72904 Cleanup unused python programs Mark DePristo 2012-03-22 20:59:14 -0400
  • 9ddd5aec93 More eval modules being removed from VariantEval Mark DePristo 2012-03-22 19:40:19 -0400
  • bd5b6d1aba Remove no longer in use Eval modules from VariantEval Mark DePristo 2012-03-22 19:38:03 -0400
  • 6c2290fb6e Performance optimization for gsa.read.gatkreport.R Mark DePristo 2012-03-22 18:46:37 -0400
  • 7faa9938b1 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-03-22 17:43:44 -0400
  • b9b9219ac7 Added respectPhaseInInput flag to RBP and integration tests Menachem Fromer 2012-03-22 17:40:21 -0400
  • 39c8edf85b Improvements to the node merging / pruning algorithm in the assembler Ryan Poplin 2012-03-22 17:16:45 -0400
  • 0a56a14d09 Build fixes to merge pool calculation models with latest interface changes. Reverted build.xml's private debug changes Guillermo del Angel 2012-03-22 16:07:07 -0400
  • b92fee711b Added missing new files from previous commit Guillermo del Angel 2012-03-22 15:47:23 -0400
  • f198cec5e2 Temp commit: new structure for pool caller, now all work is in the same framework as in UG. There's a new genotype calculation model, PoolGenotypeCalculationModel, that does all the work and plugs into UnifiedGenotyperEngine. A new AF module for pools is upcoming. Old pool caller will be removed once all work is migrated Guillermo del Angel 2012-03-22 15:46:39 -0400
  • 1dfaacfeb5 Check for consistency of the BAM and VCF sample names, with a command line disable to throw if you know what you are doing Menachem Fromer 2012-03-22 12:40:15 -0400
  • b02ef95bcf Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-03-22 12:14:12 -0400
  • 92676c63ca Make constructor of IndelGenotypeLikelihoodsCalculationModel public so it can be used in unit tests Guillermo del Angel 2012-03-22 12:13:59 -0400
  • 58965d6a6e Merged bug fix from Stable into Unstable Guillermo del Angel 2012-03-22 11:04:11 -0400
  • 256e9f001e analyzeRunReports now includes full stack traces with causes Mark DePristo 2012-03-22 10:13:47 -0400
  • b8cd959461 Potential corner condition bug fix: protect against null pointer exceptions when computing consensus indel bases when UG is discovering alt alleles. If an alt allele has non-standard bases, skip allele gracefully instead of adding null object into list Guillermo del Angel 2012-03-22 10:06:22 -0400
  • 5c98424783 Add the reference haplotype to the assembly graph. The philosophy of the assembly is now to traverse paths alongside the reference instead of finding all possible paths. Ryan Poplin 2012-03-21 17:42:54 -0400
  • a29fc6311a New debug option to output the assembly graph in dot format. Merge nodes in assembly graph when possible. Ryan Poplin 2012-03-21 15:48:55 -0400
  • 8c09ff9459 Merged bug fix from Stable into Unstable Eric Banks 2012-03-21 12:44:43 -0400
  • 58245bfa2f Bug fix: check to see whether there's a BasePileup before asking for one. Eric Banks 2012-03-21 12:44:09 -0400
  • 07c3bd32b3 Bug fix: merge NO_VARIATION records with those of another type. The sad part is that this WAS covered by integration tests but someone updated the MD5s without actually paying attention... Eric Banks 2012-03-21 12:42:13 -0400
  • dcf2fa361d Minor cleanup Eric Banks 2012-03-21 12:14:31 -0400
  • ab1c48745b Need to catch RuntimeExceptions coming out of Picard too so that they show up as UserErrors (some BAM errors are thrown as REs). Eric Banks 2012-03-21 12:13:52 -0400
  • 9e10779fa7 Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests. Ryan Poplin 2012-03-21 08:45:42 -0400
  • 0e93cf5297 Taking care of bad cigars in the GATK Mauricio Carneiro 2012-03-20 14:31:32 -0400
  • b290152542 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-03-20 08:56:04 -0400
  • 5e79046c98 Minor change but I realized from Mark's commit that the code I stole it from was flawed Eric Banks 2012-03-20 08:55:56 -0400
  • 5ecfc49f74 Minor cleanup of MergeIntervalLists (example, please look) Mark DePristo 2012-03-20 07:49:27 -0400
  • 36636eb323 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2012-03-20 07:47:24 -0400
  • ade1971581 Since we allow any generic header types, there's no longer any reason to check for supported types Eric Banks 2012-03-20 00:12:17 -0400
  • 4910ef86d9 Added a to-do for Khalid Eric Banks 2012-03-19 23:12:58 -0400
  • 5a3afd768d Walker to merge multiple bed/interval files into a single consensus. 'Walker' is used loosely here; there must be a better way to do this, but I don't know how within the GATK framework. Eric Banks 2012-03-19 22:42:48 -0400
  • 2324c5a74f Simplified the interface for simple VCF header lines by making the VCFSimpleHeaderLine not abstract anymore - now any arbitrary header line with an ID (e.g. the contig and ALT lines) can be part of this class without having to define new classes. Also, renamed the 'named' header line to 'id' since that's more accurate. Eric Banks 2012-03-19 21:29:24 -0400
  • 069ccdfdd4 Fixing broken HC integration tests while changes to exact model are being formulated. Ryan Poplin 2012-03-19 16:56:51 -0400
  • 633b5c687d Fixing MD5's (new GATKReport header was missing from old md5's) Mauricio Carneiro 2012-03-19 15:27:15 -0400
  • 9cf4df15e5 BQSR recal script (just so we can scatter-gather) Mauricio Carneiro 2012-03-19 13:28:43 -0400
  • 875dc5ef95 Re-added non-verbose MultiallelicSummary to HSP eval. Khalid Shakir 2012-03-19 14:40:31 -0400
  • e8b083ac20 Merged bug fix from Stable into Unstable Khalid Shakir 2012-03-19 14:37:36 -0400
  • d0056d6c71 Updated HSP dbsnp from 132 to 135 along with other minor patches. Khalid Shakir 2012-03-19 14:36:38 -0400
  • 7afb333811 GATK Report code cleanup Roger Zurawicki 2012-03-18 01:05:49 -0400
  • 0d4ea30d6d Updating the BQSR Gatherer to the new file format Mauricio Carneiro 2012-03-18 22:31:54 -0400
  • 37d979d98d GATK performance over time includes GATK 1.5 Mark DePristo 2012-03-18 19:49:26 -0400
  • 1c67a62fc0 Updating LikelihoodCalculationEngineUnitTest Ryan Poplin 2012-03-18 16:39:58 -0400
  • 943b1d34f8 intermediate commit to aid in debugging HC / exact model changes. HC integration tests will still fail Ryan Poplin 2012-03-18 15:50:27 -0400
  • c4f4d16490 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-03-18 14:27:42 -0400
  • 9223e451a3 Merged bug fix from Stable into Unstable Eric Banks 2012-03-18 00:54:19 -0400
  • 5c5d8e7cd3 Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on. Eric Banks 2012-03-18 00:53:29 -0400
  • 344a938a70 When checking to make sure that we have cached enough data in the PL array, use the converted index value since that's what will be used as an index into the array. Eric Banks 2012-03-18 00:36:30 -0400
  • 4f2f1cbca9 misc optimizations to the HMM code related to allocating and initializing the big state space arrays Ryan Poplin 2012-03-17 14:07:11 -0400
  • a27a9ccba2 Merged bug fix from Stable into Unstable Guillermo del Angel 2012-03-16 21:15:30 -0400
  • a05a7f287d TMP: disable checking of whether on the fly index is equal to index after run completed Guillermo del Angel 2012-03-16 21:14:45 -0400
  • 539d51f324 Resolving conflicts Eric Banks 2012-03-16 14:36:07 -0400
  • be9e48ba29 Merged bug fix from Stable into Unstable Eric Banks 2012-03-16 14:33:53 -0400
  • a7578e85e8 Rewriting a few of the indel integration tests for multi-allelics. The old tests were running b37 calls against a b36 reference, so the calls were all ref. The new tests are run against the pilot1 data and then those calls are fed back into the the same bam to test genotype given alleles, with a sprinkling of bi- and tri-allelics. Eric Banks 2012-03-16 14:21:27 -0400
  • ec4a870a0f Added @PG tag to ReduceReads Mauricio Carneiro 2012-03-16 14:09:07 -0400
  • e4cbeddf2d adding on-the-fly recalibration test data Mauricio Carneiro 2012-03-16 13:18:16 -0400
  • 3bfca0ccfd BitSet implementation of the on-the-fly recalibration using the CSV format file. Mauricio Carneiro 2012-03-08 14:52:28 -0500
  • ca11ab39e7 BitSets keys to lower BQSR's memory footprint Mauricio Carneiro 2012-03-05 17:37:34 -0500
  • 7424041a17 Updating integration tests to deal with the new GL framework. Now multi-allelic indel calls are correct. Eric Banks 2012-03-16 12:50:39 -0400