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• 5a9610d875 ReadShards now default to 10K (up from 1K) reads per samFile up to 250K Mark DePristo 2012-08-30 10:39:16 -0400
• 5a142fe265 After dicussion with Ryan/Eric, the Structural_Indel variant type is now gone, and has been entirely replaced with the access pattern .isStructuralIndel(). This makes it a strict subtype of indel. I agree that this method is a bit more sensible. Christopher Hartl 2012-08-30 17:57:31 -0400
• 82b2845b9f Fix: GSA-531 ApplyRecalibration writing to BCF: java.lang.String cannot be cast to java.lang.Double Mark DePristo 2012-08-30 16:56:36 -0400
• 7b4caec8cb Fix: GSA-531 ApplyRecalibration writing to BCF: java.lang.String cannot be cast to java.lang.Double Mark DePristo 2012-08-30 16:56:36 -0400
• 863a3d73b8 Added ThreadSafeMapReduce interface, super of TreeReducible Mark DePristo 2012-08-30 16:21:17 -0400
• 59508f8266 tasking for n threads should give you n threads in NanoScheduler, not n - 1 Mark DePristo 2012-08-30 15:57:29 -0400
• 27d1c63448 Reduce the number of test combinations in ReadBasedREferenceOrderedView Mark DePristo 2012-08-30 15:56:58 -0400
• 72cf6bdd9f Fix GSA-529: Fix RODs for parallel read walkers Mark DePristo 2012-08-30 15:10:58 -0400
• 7f166c3198 Bugfix to compareTo and equals in GenomeLoc Mark DePristo 2012-08-30 15:07:02 -0400
• 7b366d4049 misc cleanup in active region traversal. Ryan Poplin 2012-08-30 11:01:01 -0400
• 792092b891 ReadShards now default to 10K (up from 1K) reads per samFile up to 250K Mark DePristo 2012-08-30 10:39:16 -0400
• 76853806b0 Print out the time when downloads finished from S3 Mark DePristo 2012-08-30 10:10:29 -0400
• 21dd70ed36 Test to ensure that ReadBasedReferenceOrderedView produces stateless objects Mark DePristo 2012-08-30 10:10:00 -0400
• ce3d1f89ea ReadShard are no longer allowed to span multiple contigs Mark DePristo 2012-08-29 18:43:02 -0400
• a3f443c1cc Part 4 of GSA-462: Consistent RODBinding access across Ref and Read trackers Mark DePristo 2012-08-29 17:52:29 -0400
• 53376b9423 Part III of GSA-462: Consistent RODBinding access across Ref and Read trackers Mark DePristo 2012-08-29 17:44:35 -0400
• 1200848bbf Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers Mark DePristo 2012-08-29 17:39:32 -0400
• 972be8b4a4 Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers Mark DePristo 2012-08-29 16:58:21 -0400
• 8fc6a0a68b Cleanup RefMetaDataTracker before refactoring ReadMetaDataTracker Mark DePristo 2012-08-29 09:25:05 -0400
• b85ded8389 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-30 10:11:48 -0400
• 650ff29e62 oops, I meant to use binary OR here. Ryan Poplin 2012-08-30 10:11:29 -0400
• 57d997f06f Fixing bug from when FragmentUtils merging function moved over to the soft clipped start instead of the unclipped start Ryan Poplin 2012-08-30 10:10:43 -0400
• f9bab37015 Merged bug fix from Stable into Unstable Ryan Poplin 2012-08-30 09:21:24 -0400
• eb63221875 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Ryan Poplin 2012-08-30 09:19:35 -0400
• 81d5eca975 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-30 09:10:56 -0400
• 35baf0b155 This along with Mauricio's previous commit (thanks!) fixes GSA-522. There are no longer any modifications to reads in the map calls of ActiveRegion walkers. Added the bam which identified this error as a new integration test. Ryan Poplin 2012-08-30 09:07:36 -0400
• 1acf0f0b2c Fixing bug in fasta .fai generation: trim the contig names to the first whitespace if one appears. We now generate indexes identical to samtools. Eric Banks 2012-08-29 22:36:27 -0400
• 4d38befe86 Merged bug fix from Stable into Unstable Eric Banks 2012-08-29 15:13:56 -0400
• 150a969279 Be careful with String manipulation when constructing alleles in SomaticIndelDetector Eric Banks 2012-08-29 15:13:28 -0400
• ce55ba98f4 Don't try to left align indels in unmapped reads (which for some reason can still have CIGARs) because the ref context is null. Eric Banks 2012-08-29 15:01:11 -0400
• 4ea38bbfe8 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-08-29 11:39:30 -0400
• b132a33dac Delocalized BQSR now BAQs the reads on the fly instead of on input. Ryan Poplin 2012-08-29 11:39:07 -0400
• 69b56e11c8 ReadClipper won't modify the original read Mauricio Carneiro 2012-08-28 13:33:28 -0400
• e12ae65d33 Changing the commenting style in the BQSR Ryan Poplin 2012-08-29 11:27:45 -0400
• 19cc0b373e Some code review comments for Ryan Mark DePristo 2012-08-28 17:06:08 -0400
• f45226f01e Updated HSPTest expected values to match FS changes in depristo's 3baf52 commit. Khalid Shakir 2012-08-28 16:29:21 -0400
• 6d6ca090c6 RecalDatums now hold doubles so the test for equality needs an epsilon. Ryan Poplin 2012-08-28 16:00:52 -0400
• 18eca3544e Initial commit of the delocalized BQSR written as a read walker. Ryan Poplin 2012-08-28 15:24:20 -0400
• e74c527d47 Register the depricated walkers as depricated starting in v2.2 so that users get a helpful error message Eric Banks 2012-08-28 10:19:18 -0400
• 67d348a31d Retiring the alignment walkers and related integration test since we don't want to support them anymore. Eric Banks 2012-08-28 10:16:49 -0400
• 0f4acaae1b Update MD5s with new FS score Mark DePristo 2012-08-28 08:05:16 -0400
• 4b8d9c3915 Actually load the library necessary to compactPDF Mark DePristo 2012-08-28 08:05:05 -0400
• 2996693c9f FisherStrand now computed with and without filtering low-qual bases, and least significant pvalue is kept Mark DePristo 2012-08-27 20:57:44 -0400
• bedcdbdc5f Fixing merge conflict Eric Banks 2012-08-27 12:16:51 -0400
• 3d476487c6 LIBS is totally busted for deletions. Putting a check in AD for bad pileup event bases so that we don't produce busted alleles. We must fix LIBS ASAP. Eric Banks 2012-08-27 12:13:12 -0400
• 63a9ae817a Ensure thread-safety of CachingIndexedFastaSequenceFile Mark DePristo 2012-08-27 12:11:38 -0400
• e5b1f1c7f4 Add simple main function to unit test so we can run the nano scheduler test from the command line Mark DePristo 2012-08-27 09:24:16 -0400
• 2d1ea7124b One less Queue command line requirement: -tempDir now defaults to .queue/tmp. Also moved queueScatterGather to .queue/scatterGather. Khalid Shakir 2012-08-27 12:04:50 -0400
• 68c5142d2d numThreads > 1 any time you have -nt > 1 silly Mark DePristo 2012-08-26 14:36:13 -0400
• faacacd6c0 Increase runtime of nano scheduler tests to 1 min Mark DePristo 2012-08-26 08:42:58 -0400
• 846e0c11bc Add TimeOuts to new threading tests, in case there's a underlying deadlock Mark DePristo 2012-08-26 08:18:43 -0400
• fde9824765 Optimizations for parallel read walkers Mark DePristo 2012-08-25 17:21:02 -0400
• 5066b14335 Parallel FlagStat Mark DePristo 2012-08-25 17:19:57 -0400
• af540888f1 Limited version of parallel read walkers Mark DePristo 2012-08-25 16:48:22 -0400
• e060b148e2 Minor cleanup of TraverseReads Mark DePristo 2012-08-25 15:36:04 -0400
• 275a5e5439 More tests for NanoScheduler Mark DePristo 2012-08-25 15:33:01 -0400
• 6db0988898 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2012-08-25 15:40:32 -0400
• db2e88c7cb Fix for badIndelLength() throwing NPE at non-indel sites. Added integration test. Christopher Hartl 2012-08-25 12:38:23 -0700
• 59b5913b54 Merged bug fix from Stable into Unstable Mark DePristo 2012-08-25 14:53:22 -0400
• dcc972a557 Usability cleanup for BQSR Mark DePristo 2012-08-25 14:53:00 -0400
• 1044ddbc26 Minor improvement in naming of BQSR tests Mark DePristo 2012-08-25 14:06:34 -0400
• 58ca3f61df Fix horrible bug in the classification of runs as successes, sting-exceptions, or user-exceptions in analyzeRunReports Mark DePristo 2012-08-25 14:06:06 -0400
• b59948709f Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated. Christopher Hartl 2012-08-25 08:48:27 -0700
• 0996bbd548 Comments for Chris on cleanup Mark DePristo 2012-08-24 16:04:58 -0400
• 649b82ce85 Merge branch 'nanoScheduler' Mark DePristo 2012-08-24 15:59:36 -0400
• 801b910b9e GATKPerformanceOverTime is finalized (mark II) Mark DePristo 2012-08-24 15:57:45 -0400
• 62aa0ac77e GATKPerformanceOverTime is finalized Mark DePristo 2012-08-24 09:20:32 -0400
• 3bbdccb0ae Refactor and cleanup GATKPerformanceOverTime Mark DePristo 2012-08-23 21:11:15 -0400
• 9f0eff4c4c MySQLdb required to run analyzeRunReports, despite my best efforts Mark DePristo 2012-08-23 21:08:32 -0400
• 9de8077eeb Working (efficient?) implementation of NanoScheduler Mark DePristo 2012-08-24 15:34:23 -0400
• 752f44c332 Code cleanup in MVLR and SelectVariants. Should fix JIRA GSA-509 and GSA-510 Christopher Hartl 2012-08-24 12:25:11 -0700
• d6e6b30caf Initial implementation of GSA-515: Nanoscheduler Mark DePristo 2012-08-24 14:07:44 -0400
• 0545664f91 Fix ClassCastException seen in Tableau errors Eric Banks 2012-08-24 13:45:48 -0400
• b3fd74f0c4 HaplotypeCaller forbids BAQ Mark DePristo 2012-08-24 13:25:05 -0400
• 740520c23b Fix BQSR docs Eric Banks 2012-08-24 13:20:10 -0400
• 5f8574bd15 Fixing typo in error message. Ryan Poplin 2012-08-24 10:48:41 -0400
• c689d6dcac GATKPerformanceOverTime is finalized Mark DePristo 2012-08-24 09:20:32 -0400
• 8371362f3c Refactor and cleanup GATKPerformanceOverTime Mark DePristo 2012-08-23 21:11:15 -0400
• b6cc615890 MySQLdb required to run analyzeRunReports, despite my best efforts Mark DePristo 2012-08-23 21:08:32 -0400
• 1999b95754 Work around for GSA-513: ClassCastException in VariantEval Mark DePristo 2012-08-23 18:14:10 -0400
• f1166d6d00 Spotted a potential bug where sample IDs passed in from the meta data were only checked against the sample IDs in the VCF header if the input file happened to be a meta data file rather than a fam file. Added a check for fam files as well, and added an integration test to cover each case. Christopher Hartl 2012-08-23 11:43:19 -0700
• 2ae5ec5596 Update for GSA-506: Add nt and efficiency information to GATKRunReport Mark DePristo 2012-08-23 12:53:22 -0400
• 857b11b26f Done with GSA-506: Add nt and efficiency information to GATKRunReport Mark DePristo 2012-08-23 09:59:37 -0400
• 0b735884db Cleanup code in VariantContext Mark DePristo 2012-08-23 08:55:27 -0400
• d973863039 GATKPerformanceOverTime includes longer running tests for select variants and variant eval Mark DePristo 2012-08-23 08:46:42 -0400
• e5df91aa23 Looks like the @WalkerName annotation doesn't work with the GATK docs, so I'm renaming the walkers. Eric Banks 2012-08-22 20:17:39 -0400
• 95a1337285 Merge branch 'threadMonitors' Mark DePristo 2012-08-22 16:54:47 -0400
• 63af0cbcba Cleanup GATK efficiency monitor classes Mark DePristo 2012-08-22 16:45:53 -0400
• 1d47d2b573 Fix GATKPerformanceOverTime for BQSR file path error Mark DePristo 2012-08-22 16:44:30 -0400
• e1293f0ef2 GSA-507: Thread monitoring refactored so it can work without a thread factory Mark DePristo 2012-08-22 11:31:14 -0400
• f876c51277 Separately track time spent doing user and system CPU work Mark DePristo 2012-08-22 10:28:27 -0400
• 18060f237b Add thread efficiency monitoring to GATK HMS Mark DePristo 2012-08-22 09:10:09 -0400
• 27842ba448 run_performance_tests use bsub and gsa Mark DePristo 2012-08-21 16:26:12 -0400
• d7a6cd99cd Expand intervals processed for many GATKPerformanceOverTime commands Mark DePristo 2012-08-21 16:25:31 -0400
• 1aa856e0e3 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-08-22 15:53:47 -0400
• e29469eeeb Forgot to update 2 integration test md5's (in this cases, changes are legit because of the code revamp of AD, it's simpler if AD is not output when a site is not variant, as genotype DP conveys the same information) Guillermo del Angel 2012-08-22 15:53:33 -0400
• b1b9c0b132 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-08-22 15:26:39 -0400
• fe3069b278 Merged bug fix from Stable into Unstable Ryan Poplin 2012-08-22 14:40:34 -0400
• e5cfdb4811 Bug fix for popular _Duplicate allele added to VariantContext_ error reported on the forum. It seems to be due to lower case bases in the reference being treated as reference mismatches. We would try to turn these mismatches into SNP events, for example c/C. We now uppercase the result from IndexedFastaSequenceFile.getSubsequenceAt() Ryan Poplin 2012-08-22 14:39:35 -0400
• 63213e8eb5 Expanding the HaplotypeCaller integration tests to cover a wider range of data Ryan Poplin 2012-08-22 14:18:44 -0400