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  • e7553545ef Initial updates for ReadShard Joel Thibault 2013-01-03 13:57:36 -0500
  • 14a3ac0e3c Enable the use of alternate shards Joel Thibault 2013-01-02 17:01:21 -0500
  • 4cc372f53b LocusShardDataProvider doesn't need its own GenomeLocParser Joel Thibault 2012-12-21 15:14:50 -0500
  • ffbd4d85f2 No need to pass fields as parameters Joel Thibault 2012-12-14 17:37:29 -0500
  • 47e620dfbc Create BAM index to test shard boundaries Joel Thibault 2012-12-19 14:55:34 -0500
  • c1ba12d71a Added unit test for outputting sorted GATKReport Tables Tad Jordan 2013-01-03 16:25:57 -0500
  • 10a705b27f Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2013-01-03 13:42:31 -0500
  • 2018285a39 better error message Ami Levy-Moonshine 2013-01-03 13:41:03 -0500
  • c7039a9b71 Pushing in implementation of the Bayesian estimate of Qemp for the BQSR. Eric Banks 2013-01-02 15:21:44 -0500
  • 03294ae1c8 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Chris Hartl 2013-01-02 15:11:30 -0500
  • ea2d9aa4fe Merge branch 'incoming' Chris Hartl 2013-01-02 15:10:28 -0500
  • 3753209584 One md5sum slipped past in the HC integration test. Chris Hartl 2013-01-02 15:09:28 -0500
  • c515175313 Ensure that active region extensions stay on contig Joel Thibault 2013-01-02 14:10:55 -0500
  • dcb7735d3c Active Region extensions must stay on contig Joel Thibault 2013-01-02 13:46:33 -0500
  • 09199366b7 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Chris Hartl 2013-01-02 14:44:49 -0500
  • e1d09ab0db QD is now divided by the average length of the alternate allele (weighted by the allele count). The average length is stored in a related annotation, "AAL", which can be used to re-compute the "old" QD by simple multiplication. Integration tests *should* all pass. Chris Hartl 2013-01-02 14:41:29 -0500
  • a15f368bdc Re-enable testIsActiveRangeLow/High Joel Thibault 2013-01-02 10:10:09 -0500
  • 7188a4a921 Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable Chris Hartl 2013-01-02 11:39:53 -0500
  • 12f4c6307e AutoFormattingTime cleanup and complete unittests Mark DePristo 2013-01-02 08:46:11 -0500
  • c1c5737f80 Re-enabling contracts in tests in build.xml Mark DePristo 2013-01-02 11:28:54 -0500
  • 3d1c107f9d Detect if clover is present in build.xml. Automatically clean clover db in ant clean, if present Mark DePristo 2012-12-31 09:24:01 -0500
  • 429567cd3f Rename to TraverseActiveRegionsUnitTest Joel Thibault 2013-01-01 19:20:30 -0500
  • 57d38aac8a Temporarily disable due to unknown contracts problem Joel Thibault 2013-01-01 18:36:56 -0500
  • 7748b3816f Delete the test BAI file as well as the BAM Joel Thibault 2012-12-31 17:22:57 -0500
  • 5afeb465aa TODOs Joel Thibault 2012-12-20 09:52:37 -0500
  • 03780578bc Archiving SomaticIndelDetector, RemapAlignments, ReadPair, and associated library code Mark DePristo 2012-12-29 14:37:22 -0500
  • 5558a6b8f7 Deleting / archiving no longer classes Mark DePristo 2012-12-29 14:34:17 -0500
  • 38cc496de8 Move SomaticIndelDetector and associated tools and libraries into private/andrey package Mark DePristo 2012-12-29 14:34:08 -0500
  • 5f84a4ad82 Clover report excludes test files and other non-interesting files from the clover reports Mark DePristo 2012-12-24 16:31:47 -0500
  • f450cbc1a3 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ami Levy-Moonshine 2012-12-27 21:23:59 -0500
  • 609ad7dbab can't override var help Ami Levy-Moonshine 2012-12-27 15:10:33 -0500
  • 3c972175fc add tsv option to RRScript Ami Levy-Moonshine 2012-12-27 14:50:01 -0500
  • 53f8be96d2 add tsv option to RRScript Ami Levy-Moonshine 2012-12-27 14:37:54 -0500
  • 275575462f Protect against non-standard ref bases. Ryan, please review. Eric Banks 2012-12-26 15:46:21 -0500
  • 75d5b88a3d Enabling the Recal Report unit test (which looks like it was never ever enabled) Eric Banks 2012-12-26 15:35:50 -0500
  • efceb0d48c Check for well-encoded reads while fixing mis-encoded ones Eric Banks 2012-12-26 14:30:51 -0500
  • fe427cdd77 add few queue script and the CatVariantsGatherer scala class Ami Levy-Moonshine 2012-12-26 13:06:36 -0500
  • f2b7c6f0e1 Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable Chris Hartl 2012-12-26 09:20:32 -0500
  • 64c3a0ff62 Remove dependance on clover in build.xml Mark DePristo 2012-12-24 13:53:29 -0500
  • af9746af52 Fix merge failure Mark DePristo 2012-12-24 13:43:04 -0500
  • 04cc75aaec Minor cleanup and expansion of the RecalDatum unit tests Mark DePristo 2012-12-24 13:26:58 -0500
  • 7ec7a5d6b6 Misc. improvements to clover in build.xml Mark DePristo 2012-12-24 11:27:32 -0500
  • 7bf1f67273 BQSR optimization: read group x quality score calibration table is thread-local Mark DePristo 2012-12-24 10:46:47 -0500
  • 7d250a789a ArtificialReadPileupTestProvider now creates GATKSamRecords with good header values Mark DePristo 2012-12-23 08:54:27 -0500
  • 295455eee2 NanoScheduler optimizations and simplification Mark DePristo 2012-12-23 08:53:49 -0500
  • aa3ee29929 Handle case where the ReadGroup is null in GATKSAMRecord Mark DePristo 2012-12-22 13:13:01 -0500
  • bf81db40f7 NanoScheduler reducer optimizations Mark DePristo 2012-12-22 11:49:30 -0500
  • 161487b4a4 MapResult compareTo() is now unit tested Mark DePristo 2012-12-21 10:51:24 -0500
  • 940816f16a GATKSamRecord now checks that the read group is a GATKReadGroupRecord, and if not makes one Mark DePristo 2012-12-21 10:50:56 -0500
  • 14944b5d73 Incorporating clover into build.xml Mark DePristo 2012-12-20 14:53:58 -0500
  • 7796ba7601 Minor optimizations for NanoScheduler Mark DePristo 2012-12-20 12:34:05 -0500
  • 0f04485c24 NanoScheduler optimization: don't use a PriorityBlockingQueue for the MapResultsQueue Mark DePristo 2012-12-19 16:17:51 -0500
  • b92f563d06 NanoScheduler optimization for TraverseReadsNano Mark DePristo 2012-12-19 15:51:51 -0500
  • f849910c4e BQSR optimization: only compute BAQ when there's at least one error to delocalize Mark DePristo 2012-12-19 15:39:58 -0500
  • eedc01ff22 BQSRPerformanceOverTime Qscript to asseess how much we are improving BQSR Mark DePristo 2012-12-19 09:31:07 -0500
  • 0f0188ddb1 Optimization of BQSR Mark DePristo 2012-12-19 08:15:42 -0500
  • f6d5499582 The GATK engine now ensures that incoming GATKSAMRecords have GATKSAMReadGroupRecord objects in their header Mark DePristo 2012-12-18 15:46:34 -0500
  • 8be01af145 add the new gather tool to GATKExtensionsGenerator Ami Levy-Moonshine 2012-12-21 15:09:00 -0500
  • 3ca3fd4b3e keep working on loglessHMM in UG Ami Levy-Moonshine 2012-12-21 11:06:12 -0500
  • 6590039bc3 add fast gather to UG; change UG to work with log-lessHMM (work in prograss) Ami Levy-Moonshine 2012-12-20 14:58:57 -0500
  • c8cd6ac465 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2012-12-20 14:58:04 -0500
  • a098888f4d Updating missed UG md5 Ryan Poplin 2012-12-20 14:57:53 -0500
  • b491c177ff Added functionality of outputting sorted GATKReport Tables Tad Jordan 2012-12-14 12:12:10 -0500
  • b0cb513793 Adding a manual reviews file for the NA12878 knowledge base Ryan Poplin 2012-12-20 11:54:23 -0500
  • d7dc370160 Re-enabling 1000G exome chip in the KB now that we have a good copy of the VCF Eric Banks 2012-12-20 00:16:33 -0500
  • 6c3f5eefe9 Merged bug fix from Stable into Unstable Eric Banks 2012-12-19 22:29:21 -0500
  • 22d13ccdab Bug fix for Queue LSF v8.3 xingwei2012 2012-12-17 17:54:03 +0000
  • 828232d8d7 Fix a few fully-qualified usages of VariantContext classes in the HybridSelectionPipeline David Roazen 2012-12-19 16:42:35 -0500
  • a5f0fb3c4f Added some reviews manually Eric Banks 2012-12-19 15:22:12 -0500
  • 58e7a7f6f3 Don't use exome chip for NA12878 KB because it's bad data Eric Banks 2012-12-19 14:26:39 -0500
  • 4e173ef3b3 Merged bug fix from Stable into Unstable Eric Banks 2012-12-19 11:47:50 -0500
  • 4a7e0427a3 Pushing the RR bug fix that I puished into unstable into stable, as requested by Tim Eric Banks 2012-12-19 11:47:16 -0500
  • 54e5c84018 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2012-12-19 11:31:40 -0500
  • aa39037be8 updating UG integration tests. Ryan Poplin 2012-12-19 11:31:35 -0500
  • e6797d2869 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Eric Banks 2012-12-19 11:02:19 -0500
  • 70479cb71d RR bug fix: we were failing when a read started with an insertion just at the edge of the consensus region. Eric Banks 2012-12-19 10:59:07 -0500
  • f2f8172d0c Merged bug fix from Stable into Unstable David Roazen 2012-12-19 10:39:21 -0500
  • 07b369ca7e Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package David Roazen 2012-12-18 14:56:48 -0500
  • cda0c48570 auto-merge Ryan Poplin 2012-12-19 10:12:49 -0500
  • 92185dd5f4 updating HC integration tests. Ryan Poplin 2012-12-19 10:12:07 -0500
  • 3ad45223be Avoid db naming collisions when running multiple instances of na12878kb tests concurrently David Roazen 2012-12-17 16:13:03 -0500
  • 46c7ea834d Updating lftp script based on new alignment.index format Eric Banks 2012-12-19 09:50:09 -0500
  • 1ca13f9581 Fundamentally better model for the NanoScheduler Mark DePristo 2012-12-17 21:01:50 -0500
  • d0cd29cb36 Merged bug fix from Stable into Unstable David Roazen 2012-12-19 02:20:28 -0500
  • 393117a596 Revert "Merged bug fix from Stable into Unstable" David Roazen 2012-12-19 02:15:35 -0500
  • 8221b5e8c1 Merged bug fix from Stable into Unstable David Roazen 2012-12-19 02:11:32 -0500
  • 0d93330ab9 Fix bug in the PerSampleDownsamplingReadsIterator that could lead to excessive memory usage at traversal startup David Roazen 2012-12-18 23:34:23 -0500
  • a29df3e094 oops Joel Thibault 2012-12-18 19:03:12 -0500
  • ee22c1bf44 More TODOs Joel Thibault 2012-12-18 18:45:36 -0500
  • 2b1db519d7 Add reads which overstep a boundary by a single base Joel Thibault 2012-12-18 18:32:48 -0500
  • 9828b2990f Reads off the end of a contig fail SAM validation when using actual BAMs Joel Thibault 2012-12-18 17:37:36 -0500
  • 72e2394b26 Create actual BAM Joel Thibault 2012-12-01 11:08:34 -0500
  • d69d1f8988 Fun with varargs Joel Thibault 2012-12-18 13:38:10 -0500
  • 1158c1529f Refactor region/read comparisons Joel Thibault 2012-12-18 10:35:07 -0500
  • c86f5e46b0 Merge pull request #9 from yfarjoun/speedy eitanbanks 2012-12-18 15:31:11 -0800
  • 6ed9eb3da9 GATKBAMIndex now passes unit test! Problem was that SeekableBufferedStream seems to have a bug: it will read beyond the end of a file if asked to. Yossi Farjoun 2012-12-18 17:22:34 -0500
  • 902ca7ea70 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Ryan Poplin 2012-12-18 15:45:33 -0500
  • 3950f7b3e3 Increasing the INFORMATIVE_LIKELIHOOD_THRESHOLD value to 0.2 Ryan Poplin 2012-12-18 15:45:12 -0500
  • b5d590ba92 Based on NA12878 knowledge base experiments updating HC to allow for a much smaller minimum kmer length in the assembly graph. Ryan Poplin 2012-12-18 15:43:56 -0500
  • 002ce9c1d5 Merge pull request #8 from yfarjoun/master eitanbanks 2012-12-18 10:16:53 -0800