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  • 641c6a361e Fix nasty memory leak in new data thread x cpu thread parallelism Mark DePristo 2012-09-10 16:16:19 -0400
  • 195cf6df7e Attempting to fix out of memory errors with new traversal engine creator Mark DePristo 2012-09-10 14:17:41 -0400
  • f713d400e2 Fixed GSA-515 Nanoscheduler GSA-555 / Make NT and NCT work together Mark DePristo 2012-09-09 16:52:52 -0400
  • 233f70f8ba Final cleanup of TraversalProgressMeters, moved to utils.progressmeter Mark DePristo 2012-09-09 11:00:36 -0400
  • 934bc5eb7a Better printing of log2 values for nt, as the coord_trans in ggplot isn't as nice a log2(value) display Mark DePristo 2012-09-08 20:17:52 -0400
  • 2e94a0a201 Refactor TraversalEngine to extract the progress meter functions Mark DePristo 2012-09-08 20:17:15 -0400
  • 4a84ff4fce Fix a nasty bug in reading GATK reports with a single line Mark DePristo 2012-09-08 19:45:56 -0400
  • 5bce3a738d Updated import Menachem Fromer 2012-09-10 17:01:47 -0400
  • d2f3d6d22f Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" David Roazen 2012-09-10 15:52:39 -0400
  • 0b717e2e2e Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples) Menachem Fromer 2012-09-10 15:32:41 -0400
  • 449b89bd34 Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples) Menachem Fromer 2012-09-10 15:08:44 -0400
  • 6ab305fa4f Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples) Menachem Fromer 2012-09-10 15:06:07 -0400
  • ac8a4dfc2d The comprehensive LIBS unit test is now truly comprehensive (or it would be if LIBS wasn't busted). The test can handle a read with any arbitrary legal CIGAR and iterates over the elements/bases in time with the real LIBS, failing if there are any differences. I've left the few hard-coded CIGARs in there for now with a note to move to all possible permutations once we move to fix LIBS (otherwise the tests would fail now). Eric Banks 2012-09-10 15:04:06 -0400
  • aa9829b55c fixing typo Ryan Poplin 2012-09-10 13:36:37 -0400
  • a13e645854 Incorporating readStrand into indel calculation in delocalized BQSR. Skipping all of the overlapping events, not just the start of the event. Ryan Poplin 2012-09-10 12:53:45 -0400
  • 10c720cbba Merge branch 'master' of ssh://gsa4/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-09-10 09:56:47 -0400
  • d7499e0642 Updating the rank sum test documentation Eric Banks 2012-09-09 22:17:36 -0400
  • 2d4b00833b Bug fix for logging likelihoods in new read allele map: reads which were filtered out were being excluded from map, but they should be included in annotations Guillermo del Angel 2012-09-09 20:35:45 -0400
  • 3dd0f59765 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-09-09 14:41:24 -0400
  • 36913706c0 Bug fix in HC GenotypingEngine to ensure that all the merged complex events get properly added to the priority list used by VariantContextUtils when combining multiallelic events. Ryan Poplin 2012-09-09 13:47:54 -0400
  • 688fc9fb56 Bug fix in HC GenotypingEngine to ensure that all the merged complex events get properly added to the priority list used by VariantContextUtils when combining multiallelic events. Ryan Poplin 2012-09-09 10:36:09 -0400
  • 8ca205f1a9 Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-09-07 14:26:06 -0400
  • b1677fc719 Fixed JIRA GSA-520 for Guillermo: when intervals with zero coverage were present, DiagnoseTargets was trying to merge them with the next interval (even if non-overlapping) which would cause problems later on when it checked to make sure that intervals were strictly overlapping. Eric Banks 2012-09-07 14:25:57 -0400
  • 3f2a4379af Added forum API version stub to base URL for posting GATKDocs Geraldine Van der Auwera 2012-09-06 15:10:35 -0400
  • ed3d9b050f Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-09-07 11:45:09 -0400
  • 3dc248a49d Adding another test Eric Banks 2012-09-07 11:41:38 -0400
  • 81b27f9db2 auto-merging to latest version Ryan Poplin 2012-09-07 11:36:47 -0400
  • 41a8a304a0 Catch masked OutOfMemory errors as User Errors Eric Banks 2012-09-07 11:27:00 -0400
  • f25bf0f927 EfficiencyMonitoringThreadFactoryUnitTests thing keeps timing out unnecessary Mark DePristo 2012-09-07 11:03:00 -0400
  • d62eca5d92 Update GATKPerformanceOverTime to measure -nt and -nct Mark DePristo 2012-09-07 10:47:29 -0400
  • bcdbc751fe Update GATKPerformanceOverTime to measure -nt and -nct Mark DePristo 2012-09-07 10:43:55 -0400
  • bf87de8a25 UnitTests for ReducerThread and InputProducer Mark DePristo 2012-09-07 09:51:32 -0400
  • 8c0e3b1e0c UnitTests for InputProducer Mark DePristo 2012-09-07 09:12:47 -0400
  • c503884958 GSA-515 Nanoscheduler GSA-551 / Optimize nanoScheduling performance of UnifiedGenotyper Mark DePristo 2012-09-07 08:57:35 -0400
  • 9d12935986 Intermediate commit for new hyper parallel NanoScheduler Mark DePristo 2012-09-06 14:33:31 -0400
  • 576c7280d9 Extensions to the ErrorThrowing framework for testing purposes Eric Banks 2012-09-06 22:03:18 -0400
  • cb84a6473f Downsampling: experimental engine integration David Roazen 2012-05-24 09:17:11 -0400
  • 6df6c1abd5 Fix for PBT to stop NPE when there are no likelihoods present Eric Banks 2012-09-06 13:14:18 -0400
  • a7396d29c9 Final bugfixes to LDCorrectedDosage. In addition: rigorous contractification and a unit test for core functionalities. Special thanks to David for help with building and running contracts. Christopher Hartl 2012-09-06 00:52:31 -0400
  • 5ab5d8dee8 Give EfficiencyMonitoringThreadFactoryUnitTest longer to complete its tests Mark DePristo 2012-09-05 22:08:34 -0400
  • 1b064805ed Renaming -cnt to -nct for consistency Mark DePristo 2012-09-05 21:13:19 -0400
  • e77abfa82d Merge branch 'nanoScheduler' Mark DePristo 2012-09-05 21:10:08 -0400
  • 0bd2a872fa Done GSA-282: Unindexed traversals crash if a read goes off the end of a contig Mark DePristo 2012-09-04 07:26:01 -0400
  • 228bac75e4 By default do only NT tests in integration tests Mark DePristo 2012-09-05 20:57:49 -0400
  • 574a8f710b Add static boolean controlled output of individual map call timing to nanoSecond resolution Mark DePristo 2012-09-05 17:40:02 -0400
  • e11915aa0a GSA-515 Nanoscheduler GSA-550 ThreadSafeMapReduce shouldn't be super interface of TreeReducible Mark DePristo 2012-09-05 17:37:56 -0400
  • c5f1ceaa95 All read and loci traversals go through NanoScheduler now Mark DePristo 2012-09-05 16:38:21 -0400
  • dddf148a59 Fixed bug in ThreadAllocation getTotalNumberOfThreads Mark DePristo 2012-09-05 16:35:32 -0400
  • 225f3a0ebe Update integration test system to allow us to differentiate between testing data and cpu parallelism Mark DePristo 2012-09-05 16:35:00 -0400
  • 9bf1d138d9 New GATK argument interface for data and cpu threads Mark DePristo 2012-09-05 15:41:52 -0400
  • 1e55475adc NanoScheduler uses ExecutorService to run input reader thread Mark DePristo 2012-09-04 18:07:08 -0400
  • 71d9ebcb0d Fix bug (introduced by me) that didn't include contig in progress meter Mark DePristo 2012-09-04 18:03:05 -0400
  • c822b7c760 Fix long-standing NPE in LMS due to inappropriate timing of initialization Mark DePristo 2012-09-04 18:02:40 -0400
  • a997c99806 Initial NanoScheduler with input producer thread Mark DePristo 2012-09-04 17:54:43 -0400
  • 03dd470ec1 Test for progressFunction in NanoScheduler; bugfix for single threaded fast path Mark DePristo 2012-09-04 14:58:12 -0400
  • 8cdeb51b78 Cleanup printProgress in TraversalEngine Mark DePristo 2012-09-04 14:50:06 -0400
  • d503ed97ab Mark I NanoScheduling TraverseLoci Mark DePristo 2012-09-04 13:47:40 -0400
  • 757e6a0160 Making Pileup thread-safe Mark DePristo 2012-09-04 13:45:57 -0400
  • d7105223fe More debugging output for NanoScheduler when debugging is enabled Mark DePristo 2012-09-04 13:44:39 -0400
  • 9823102c0c TraverseReadsNano supports walker.filter and walker.done Mark DePristo 2012-09-02 12:16:56 -0400
  • 1a8f5fc374 Trivial cleanup of NanoScheduler Mark DePristo 2012-09-02 11:53:59 -0400
  • 6a5a70cdf1 Done GSA-539: SimpleTimer should use System.nanoTime for nanoSecond resolution Mark DePristo 2012-09-02 11:37:30 -0400
  • 59109d5eeb NanoScheduler tracks time outside of its execute call Mark DePristo 2012-09-02 10:54:18 -0400
  • 800a27c3a7 NanoScheduler tracks time within input, map, and reduce Mark DePristo 2012-09-01 12:29:59 -0400
  • 7087b22ea3 No debugging output (even conditional) for ReadTransformers in PrintReads Mark DePristo 2012-09-01 12:28:54 -0400
  • e01258b261 NanoScheduler now supports printProgress. Bugfixes to printProgress Mark DePristo 2012-09-01 11:51:31 -0400
  • 6055101df8 NanoScheduler no longer groups inputs, each map() call is interlaced now Mark DePristo 2012-08-31 20:10:26 -0400
  • 397a5551ef More memory for gatkdocs and extracthelp targets Mark DePristo 2012-08-31 19:54:33 -0400
  • e3b4cc02aa Done GSA-282: Unindexed traversals crash if a read goes off the end of a contig Mark DePristo 2012-09-04 07:26:01 -0400
  • d6884e705a Revert "fixed a typo in StringText.properties" Yossi Farjoun 2012-09-05 15:21:00 -0400
  • ad5fa449e7 fixed a typo in the string comment Yossi Farjoun 2012-09-05 14:46:10 -0400
  • f4b39a7545 Merge branch 'master' of ssh://gsa4/humgen/gsa-scr1/gsa-engineering/git/unstable Yossi Farjoun 2012-09-05 14:33:39 -0400
  • 6e517df5d9 fixed a typo in StringText.properties Yossi Farjoun 2012-09-05 14:33:08 -0400
  • df749b27c1 Bug fix in delocalized BQSR in the calculateIsIndel() function Ryan Poplin 2012-09-05 14:21:20 -0400
  • 84a83fd3f3 fixing typo Ryan Poplin 2012-09-05 10:41:03 -0400
  • fc06f39411 Fixed docs for Pileup walker Eric Banks 2012-09-05 09:55:34 -0400
  • d795437202 - New UserExceptions added for when ReadFilters or Walkers specified on the command line are not found. When -rf xxxx cannot find the class corresponding to xxxx, all read filters are printed in a better formatted way, with links to their gatk docs. - VariantAnnotatorEngine changed to call genotype annotations even if pilups and allele -> likelihood mappings are not present. Current genotype annotations altered to check for null pilupes and null mappings. Christopher Hartl 2012-09-04 16:41:44 -0400
  • 9cc1a9931b Resolving merge conflicts. Ryan Poplin 2012-09-04 10:47:38 -0400
  • c9944d81ef Skip array needs to also be used in the updateDataForRead function of the delocalized BQSR. Ryan Poplin 2012-09-04 10:33:37 -0400
  • 0892f2b8b2 Closing GSA-287:LocusReferenceView doesn't do very well in the case where contigs land off the end of the reference Mark DePristo 2012-09-03 20:18:56 -0400
  • 52d6bea804 a few more useful git ignores Mark DePristo 2012-09-01 11:08:36 -0400
  • 1b0ce511a6 Updating BQSR tests due to my change to reset BQSR calibration data Mark DePristo 2012-08-31 19:50:20 -0400
  • 277ba94c7b Update from dbsnp135 to dbsnp137. Eric Banks 2012-08-31 14:06:29 -0400
  • 5ea7cd6dcc Updating resource bundle: no reason to include both genotype and sites files for Omni and HM3, sites are enough. Also, don't include duplicate entry for the Mills indels. Eric Banks 2012-08-31 14:01:54 -0400
  • f066a02f3e Merge branch 'applyRecalibration' Mark DePristo 2012-08-31 13:43:52 -0400
  • c9ea213c9b Make BaseRecalibration thread-safe Mark DePristo 2012-08-31 13:42:29 -0400
  • 27ddebee53 Protect PrintReads from strange state from TraverseReadsUnitTests Mark DePristo 2012-08-31 13:41:03 -0400
  • e028901d54 Fixed bad contract in ReadTransformer Mark DePristo 2012-08-31 13:40:33 -0400
  • cf91d894e4 Fix build problems with tests Mark DePristo 2012-08-31 11:56:40 -0400
  • 817ece37a2 General infrastructure for ReadTransformers Mark DePristo 2012-08-31 11:42:50 -0400
  • ff6ebbf3fd Resolving merge conflicts. Ryan Poplin 2012-08-31 11:25:55 -0400
  • e22bd09477 Initial fix for delocalized BQSR to make it work with new RefMetaDataTracker Ryan Poplin 2012-08-31 11:23:08 -0400
  • 143fbead03 Adding an experimental format field annotation that calculates the per-sample residual dosage after accounting for LD. It's meant to be run in a single pass over a chromosome, for instance. Christopher Hartl 2012-08-31 04:04:00 -0400
  • ac0c44720b I started to put together a set of unit tests for the PileupElement creation functionality of LocusIteratorByState and found pretty quickly that it's definitely still busted for indels. The data provider is nowhere near comprehensive yet, but I need to sit back and think about how to really test some of the functionality of LIBS. Committing what I have for now because at the very least it'll be helpful going forward (failing tests are commented out with TODO). Eric Banks 2012-08-30 22:49:13 -0400
  • 39400c56a9 Update md5s for VQSR, as VQSLOD is now a double and gets the standard double precision treatment in VCF Mark DePristo 2012-08-30 19:41:36 -0400
  • 2f749b5e52 Added ThreadSafeMapReduce interface, super of TreeReducible Mark DePristo 2012-08-30 16:21:17 -0400
  • 544740d45d tasking for n threads should give you n threads in NanoScheduler, not n - 1 Mark DePristo 2012-08-30 15:57:29 -0400
  • 1212dfd2ef Reduce the number of test combinations in ReadBasedREferenceOrderedView Mark DePristo 2012-08-30 15:56:58 -0400
  • 7a462399ce Fix GSA-529: Fix RODs for parallel read walkers Mark DePristo 2012-08-30 15:10:58 -0400
  • 7d95176539 Bugfix to compareTo and equals in GenomeLoc Mark DePristo 2012-08-30 15:07:02 -0400