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  • e877db8f42 Changed visibility of getSampleDB from protected to public as the sampleDB needs to be accessible from Annotators and Evaluators too. Laurent Francioli 2011-11-28 17:11:30 +0100
  • 5c2595701c Added a function to get families only for a given list of samples. Laurent Francioli 2011-11-28 17:10:33 +0100
  • 3c36428a20 Bug fix for TiTv calculation -- shouldn't be rounding Mark DePristo 2011-11-28 10:20:34 -0500
  • 436b4dc855 Updated docs Eric Banks 2011-11-28 08:59:48 -0500
  • b1dd632d5d Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Laurent Francioli 2011-11-25 16:16:44 +0100
  • e60272975a Fix for changed MD5 in streaming VCF test Mark DePristo 2011-11-23 19:01:33 -0500
  • 12f09d88f9 Removing references to SimpleMetricsByAC Mark DePristo 2011-11-23 16:08:18 -0500
  • fdd90825a1 Queue now outputs a GATK-like header with version number, build timestamp, etc. David Roazen 2011-11-23 13:31:39 -0500
  • e319079c32 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-23 13:02:11 -0500
  • 4107636144 VariantEval updates Mark DePristo 2011-11-23 13:02:07 -0500
  • e5b85f0a78 A toString() method for IntervalBindings David Roazen 2011-11-23 11:45:57 -0500
  • 5a4856b82e GATKReports now support a format field per column Mark DePristo 2011-11-23 11:31:04 -0500
  • c8bf7d2099 Check for null comment Mark DePristo 2011-11-23 10:47:21 -0500
  • c1ea53d088 Solve merge conflicts Guillermo del Angel 2011-11-23 09:17:32 -0500
  • d2499bcc33 Cleaning up and institutionalizing several local hacks to ValidationSiteSelector: add argument to ignore polymorphic status in VC (useful when we want to intentionally select monomorphic sites), add dummy NullSampleSelector class that should be used if we really don't want to do any sample selection, and enabled sampleMode=NONE for this purpose. Guillermo del Angel 2011-11-23 09:14:10 -0500
  • 6c2555885c Caching getSimpleName() in VariantEval is a big performance improvement Mark DePristo 2011-11-23 08:34:05 -0500
  • 32adbd614f Solve merge conflict Guillermo del Angel 2011-11-22 22:48:46 -0500
  • 941f3784dc Solve merge conflict Guillermo del Angel 2011-11-22 22:48:03 -0500
  • 75d93e6335 Another corner condition fix: skip likelihood computation in case we cut so many bases there's no haplotype or read left Guillermo del Angel 2011-11-22 22:46:12 -0500
  • a3aef8fa53 Final performance optimization for GenotypesContext Mark DePristo 2011-11-22 17:19:30 -0500
  • 990c02e4de Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-22 17:19:11 -0500
  • 0fa50056eb Reorganizing package structure for compression tools (incl. Reduce Reads) Mauricio Carneiro 2011-11-22 15:03:31 -0500
  • 1a50d54c03 A walker that generates the distribution of quality scores Mauricio Carneiro 2011-11-22 14:40:56 -0500
  • 1614ca1115 Force use of LinkedList Mauricio Carneiro 2011-11-22 10:35:03 -0500
  • 38a90da92c Fixed merge conflict to Unstable Guillermo del Angel 2011-11-22 14:39:45 -0500
  • 32a77a8a56 Prevent out of bound error in case read span > reference context + indel length. Can happen in RNAseq reads with long N CIGAR operators in the middle. Guillermo del Angel 2011-11-22 13:57:24 -0500
  • 5821c11fad For BAM and Reviewed errors we now check the error message to see if it's actually a 'too many open files' problem and, if so, we generate a User Error instead. Eric Banks 2011-11-22 10:50:22 -0500
  • 5e7b9ae119 The NONE option is not supported yet (but the error message should mention this) Eric Banks 2011-11-22 10:48:38 -0500
  • 7087310373 Embarassing bug fixed Mark DePristo 2011-11-22 10:16:36 -0500
  • e484625594 GenotypesContext now updates cached data for add, set, replace operations when possible Mark DePristo 2011-11-22 08:40:48 -0500
  • 29ca24694a UG now encoding NO_CALLs as ./. not ./.:.:4:0,0,0 Mark DePristo 2011-11-22 08:22:32 -0500
  • 4ea74c42de Including GENCODE BED argument, removing CAPTURE target Mark DePristo 2011-11-21 19:18:43 -0500
  • 2b51c01df4 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-21 19:16:06 -0500
  • 5443d3634a Again, fixing the add call when we really mean replace Mark DePristo 2011-11-21 19:15:56 -0500
  • 8c7430e6ff Bugfix: isOriginalRead had the wrong check for WGS Mauricio Carneiro 2011-11-21 16:43:15 -0500
  • 756695ee3f Better Unit tests for Synthetic Reads Mauricio Carneiro 2011-11-21 16:14:56 -0500
  • 5ad3dfcd62 BugFix: byte overflow in SyntheticRead compressed base counts Mauricio Carneiro 2011-11-21 14:50:51 -0500
  • 9ea7b70a02 Added decode method to LazyGenotypesContext Mark DePristo 2011-11-21 16:21:23 -0500
  • ab2efe3bd3 Reverting bad exact model changes Mark DePristo 2011-11-21 16:14:40 -0500
  • 44554b2bfd Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-21 15:01:45 -0500
  • 022832bd74 Very bad use of the == operator with Strings was ensuring that validating GenomeLocs was very inefficient. This fix resulted in a significant speedup for a simple RodWalker. Eric Banks 2011-11-21 14:49:47 -0500
  • 1561af22af Exact model code cleanup Mark DePristo 2011-11-21 14:35:15 -0500
  • 2c501364b8 GenotypesContext no longer have immutability in constructor Mark DePristo 2011-11-21 14:34:31 -0500
  • 1296dd41be Removing the legacy -L "interval1;interval2" syntax David Roazen 2011-11-21 11:52:39 -0500
  • e467b8e1ae More contracts on LazyGenotypesContext Mark DePristo 2011-11-21 09:34:57 -0500
  • 2e9ecf639e Generalized interface to LazyGenotypesContext Mark DePristo 2011-11-21 09:30:40 -0500
  • f0ac588d32 Extensive unit test for GenotypeContextUnitTest Mark DePristo 2011-11-20 18:28:01 -0500
  • bc44f6fd9e Utility function Collection<Genotype> -> Collection<String> Mark DePristo 2011-11-20 18:26:56 -0500
  • 9445326c6c Genotype is Comparable via sampleName Mark DePristo 2011-11-20 18:26:27 -0500
  • f9e25081ab Completed documented LazyGenotypesContext Mark DePristo 2011-11-20 08:35:52 -0500
  • 9cb3fe3a59 Vastly better way of doing on-demand genotyping loading Mark DePristo 2011-11-20 08:23:09 -0500
  • f392d330c3 Proper use of builder. Previous conversion attempt was flawed Mark DePristo 2011-11-19 22:09:56 -0500
  • 7d09c0064b Bug fixes and code cleanup throughout Mark DePristo 2011-11-19 18:40:15 -0500
  • 707bd30b3f Should have been @BeforeMethod Mark DePristo 2011-11-19 16:10:09 -0500
  • 8f7eebbaaf Bugfix for pError not being checked correctly in CommonInfo Mark DePristo 2011-11-19 15:58:59 -0500
  • b7b57ef39a Updating MD5 to reflect canonical ordering of calculation Mark DePristo 2011-11-19 15:57:33 -0500
  • 73119c8e3c Merge with master Mark DePristo 2011-11-19 09:56:06 -0500
  • f685fff79b Killing the final versions of old new VariantContext interface Mark DePristo 2011-11-18 21:32:43 -0500
  • 6cf315e17b Change interface to getNegLog10PError to getLog10PError Mark DePristo 2011-11-18 21:07:30 -0500
  • c7f2d5c7c7 Final minor fix to contract Mark DePristo 2011-11-18 14:49:06 -0500
  • b5de182014 isEmpty now checks if mReadBases is null Mauricio Carneiro 2011-11-18 18:34:05 -0500
  • 8ab3ee9c65 Merge remote-tracking branch 'unstable/master' into rr Mauricio Carneiro 2011-11-18 16:50:25 -0500
  • 333e5de812 returning read instead of GATKSAMRecord Mauricio Carneiro 2011-11-18 16:49:59 -0500
  • 3f141d3c32 slightly clearer context to finalizeAndAdd() Mauricio Carneiro 2011-11-18 16:34:30 -0500
  • e08b070a6a Bug fix: Variant region starting after synthetic read didn't close it properly Mauricio Carneiro 2011-11-18 16:25:36 -0500
  • 74eeb32d74 adapting reduce reads script to do WGS Mauricio Carneiro 2011-11-18 15:04:43 -0500
  • 8bb4d4dca3 First pass of the asynchronous block loader. Matt Hanna 2011-09-13 10:49:16 -0400
  • a2e79fbe8a Fixes to contracts Mark DePristo 2011-11-18 14:18:53 -0500
  • 660d6009a2 Documentation and contracts for GenotypesContext and VariantContextBuilder Mark DePristo 2011-11-18 13:59:30 -0500
  • f54afc19b4 VariantContextBuilder Mark DePristo 2011-11-18 12:39:10 -0500
  • 6459784351 Merged bug fix from Stable into Unstable Eric Banks 2011-11-18 12:34:57 -0500
  • c62082ba1b Making this class public again as per request from Cancer folks Eric Banks 2011-11-18 12:34:27 -0500
  • 8710673a97 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-18 12:29:33 -0500
  • 768b27322b I figured out why we were getting tons of hom var genotype calls with Mauricio's low quality (synthetic) reduced reads: the RR implementation in the UG was not capping the base quality by the mapping quality, so all the low quality reads were used to generate GLs. Fixed. Eric Banks 2011-11-18 12:29:15 -0500
  • 7490dbb6eb First version of VariantContextBuilder Mark DePristo 2011-11-18 11:06:15 -0500
  • dbc1d53e7a Simple qscript to select 2000 random multiallelic indels from VQSR indel release, for array validation Guillermo del Angel 2011-11-18 10:52:09 -0500
  • 77ef2be9b8 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-11-18 07:53:13 -0500
  • 99ed64933f OK, I had it with the validation site selector running for 60 hours (due to speed of genotype reading/parsing) in gsa3 only to fail in OnTraversalDone() because of some silly operator issue. Break up validation site selection process by chromosome, pick # of sites in each chromosome proportional to chr length, (taking care of roundoff issues to ensure precisely requested number of sites is kept), and then CombineVariants in the end. This also makes the selector run comfortably under 2Gb and thus can be easily LSF'ed Guillermo del Angel 2011-11-18 07:52:52 -0500
  • f48d4cfa79 Bug fix: fully clipping GATKSAMRecords and flushing ops Roger Zurawicki 2011-11-18 00:19:59 -0500
  • fa454c88bb UnitTests for VariantContext for chrCount, getSampleNames, Order function Mark DePristo 2011-11-17 20:37:22 -0500
  • 02f22cc9f8 No more VC integration tests. All tests are now unit tests Mark DePristo 2011-11-17 15:33:09 -0500
  • 23359d1c6c Bugfix for pruneVariantContext, which was dropping the ref base for padding Mark DePristo 2011-11-17 15:32:52 -0500
  • 473b860312 Major determinism fix for UG and RankSumTest Mark DePristo 2011-11-17 15:31:45 -0500
  • 68b2a0968c Updating the HybridSelectionPipeline for SnpEff 2.0.4 RC3 David Roazen 2011-11-17 13:16:22 -0500
  • c50274e02e During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. Moved flanking interval utilies to IntervalUtils with UnitTests. Khalid Shakir 2011-11-17 13:53:46 -0500
  • bad19779b9 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-17 13:29:43 -0500
  • 16a021992b Updated header description for the INFO and FORMAT DP fields to be more accurate. Eric Banks 2011-11-17 13:17:53 -0500
  • e7d41d8d33 Minor cleanup Eric Banks 2011-11-17 12:00:28 -0500
  • 7e66677769 Expanded UnitTests for VariantContext Mark DePristo 2011-11-16 20:45:15 -0500
  • 72f00e2883 Merging Roger's Unit tests for Reduce Reads from RR repository Mauricio Carneiro 2011-11-16 17:26:49 -0500
  • aa0610ea92 GenotypeCollection renamed to GenotypesContext Mark DePristo 2011-11-16 16:24:05 -0500
  • 974daaca4d V13 version in archive. Can you pulled out wholesale for performance testing Mark DePristo 2011-11-16 16:08:46 -0500
  • caf6080402 Better algorithm for merging genotypes in CombineVariants Mark DePristo 2011-11-16 15:17:33 -0500
  • 101ffc4dfd Expanded, contrastive VariantContextBenchmark Mark DePristo 2011-11-16 13:35:16 -0500
  • f250b47228 Someone broke this for SNPs when adding support for indels Eric Banks 2011-11-16 10:49:27 -0500
  • e56d52006a Continuing bugfixes to get new VC working Mark DePristo 2011-11-16 10:39:17 -0500
  • eb8e031f75 Merged bug fix from Stable into Unstable Matt Hanna 2011-11-16 09:57:37 -0500
  • 6a5d5e7ac9 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable Matt Hanna 2011-11-16 09:57:13 -0500
  • 7ac5cf8430 Getting rid of unsupported CountReadPairs walker in stable. Removal of remainder of pairs processing framework to follow in unstable. Matt Hanna 2011-11-16 09:53:59 -0500
  • c2ebe58712 Merge remote-tracking branch 'Laurent/master' Eric Banks 2011-11-16 09:34:47 -0500