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  • 21bf8b4b93 Odd, what I saw on IntelliJ hadn't saved to sting before committing. Here's the actual change. chartl 2010-03-08 15:54:41 +0000
  • fe8a8b9199 Hooked up both optimization models via command line arguments. rpoplin 2010-03-08 14:49:59 +0000
  • cc6a714c09 Handle excess coverage in interval output chartl 2010-03-08 14:40:05 +0000
  • ca2a0266dc Converting annotation values that are set to Double.Infinity rpoplin 2010-03-08 14:04:33 +0000
  • b42e0a398e Bug fix in variant optimizer for when there are more novel variants than known variants in the callset. Changing the magic numbers related to the starting sigma values for the gaussian clusters. rpoplin 2010-03-08 13:02:08 +0000
  • e4360bac6a More comprehensive support when sharding for ref walkers. hanna 2010-03-08 11:25:20 +0000
  • eb165ca844 Celebrate the fact that the new sharding system works with integration tests by removing the scary debug line. hanna 2010-03-07 23:40:56 +0000
  • 9e107513d0 In the new sharding system, if no read group is present, hallucinate one. Added for test compatibility, but not sure whether we still need this feature. TODO: Poll the group about this feature. hanna 2010-03-07 23:01:34 +0000
  • a7fe07c404 A few stopgap fixes to get the GATK to the point where the old sharding infrastructure can be torn down: 1) New sharding system emulates old MonolithicSharding mechanism. 2) Better awareness of differences between fasta and BAM files when creating shards. hanna 2010-03-07 21:01:25 +0000
  • dd6122f682 Fixed another bug in the original sharding system. Updated integration tests as appropriate. hanna 2010-03-07 15:32:18 +0000
  • 8f4fbf29a7 Band-Aid: changed the pointers from mike's home directory to a checkout of the last know working revision r7169 in my directory. kshakir 2010-03-07 04:19:01 +0000
  • ee2ec7ced9 Fix off-by-one error in original implementation of read sharding. Tested by awking output of BamToFastq vs. samtools until the outputs matched exactly. hanna 2010-03-06 18:52:53 +0000
  • 1ef1091f7c Cleanup and simplification of read interval sharding. hanna 2010-03-05 23:34:38 +0000
  • ee913eca07 Forgot to check in fix this morning depristo 2010-03-05 21:07:19 +0000
  • 7fa0f77721 add output for number of variants that validated as true ebanks 2010-03-05 18:57:44 +0000
  • 037ac9c9af Actually calculate base counts by read group when "both" is specified. Modified integration test to cement the now-correct "both" behavior. chartl 2010-03-05 18:31:48 +0000
  • 8738c544f1 Minor refactoring of CoverageStatistics to allow simultaneous output of per-sample and per-read group statistics. chartl 2010-03-05 17:06:52 +0000
  • 95d560aa2f More incremental updates to the variant optimizer. rpoplin 2010-03-05 16:42:42 +0000
  • 7a7e85188c Better eagerDecode default. hanna 2010-03-05 16:42:23 +0000
  • 33cefddf55 Better INFO field annotation for Mendel violations depristo 2010-03-05 15:22:04 +0000
  • 9f7ebe1e1c - add name to vcf od field - don't do HW calculation if everything is a no-call ebanks 2010-03-05 01:43:01 +0000
  • 7104a3a96c Fix for accumulator exception when running reduce by interval walkers without intervals. hanna 2010-03-05 01:04:08 +0000
  • 366771d5a6 another test-with-multiple outputs fix aaron 2010-03-04 22:46:15 +0000
  • 9eb122924f misc cleanup ebanks 2010-03-04 21:34:13 +0000
  • 706d49d84c Commit for Aaron chartl 2010-03-04 21:29:07 +0000
  • c20d3e567e Now outputs fully spec-compliant VCF with proper annotations. Emits statistics as to number of good/bad records. ebanks 2010-03-04 21:28:17 +0000
  • 54f04dc541 forgot to uncomment the auto-deletion of temp files... aaron 2010-03-04 20:29:42 +0000
  • 80cc6bbeb4 add a way to test files generated by a walker that aren't command-line arguments; added some example code in CoverageStatisticsIntegrationTest for Chris. aaron 2010-03-04 20:20:58 +0000
  • adea38fd5e Sharding system fixes for corner cases generally related to lack of coverage in the BAM file. hanna 2010-03-04 18:59:21 +0000
  • a4d494c38b Add option to adhere to the PlinkRod naming convention [ProjectName]|c[Chrom]_p[Pos] chartl 2010-03-04 18:31:27 +0000
  • 0dd65461a1 Various improvements to plink, variant context, and VCF code. We almost completely support indels. Not yet done with plink stuff. ebanks 2010-03-04 17:58:01 +0000
  • c8077b7a22 Waypoint check-in: a couple of changes to for Tribble, and adding some options to the integration test for passing in auxillary files that aren’t “%s” command line options. aaron 2010-03-04 16:02:21 +0000
  • 6759acbdef Coverage statistics now fully implements DepthOfCoverage functionality, including the ability to print base counts. Minor changes to BaseUtils to support 'N' and 'D' characters. PickSequenomProbes now has the option to not print the whole window as part of the probe name (e.g. you just see PROJECT_NAME|CHR_POS and not PROJECT_NAME|CHR_POS_CHR_PROBESTART-PROBEND). Full integration tests for CoverageStatistics are forthcoming. chartl 2010-03-04 15:00:02 +0000
  • 023654696e First pass at handling SAMFileReaders using a SAMReaderID. This allows us to firewall GATK users from the readers, which they could abuse in ways that could destabilize the GATK. hanna 2010-03-04 00:59:32 +0000
  • b241e0915b Incremental update to VariantOptimizer. Refactored parts of the clustering code to make it more clear. More comments. rpoplin 2010-03-03 20:33:35 +0000
  • 073fdd8ec7 Let's try not to die suffocating when a bad region with humongous coverage is encountered. New option: -maxNumberOfReads (--mnr), with default of 10,000. If count of reads cached in the current window reaches the specified limit, the whole window is immediately shifted by the whole window length and all currently cached reads are dropped. NOTE: this also means that we are not going to call ANY indels from the current window, even though we could try using just the reads cached so far. asivache 2010-03-03 17:34:30 +0000
  • 6ca6c98980 Can just give PickSequenomProbes a dbsnp rod to mask chartl 2010-03-03 16:50:58 +0000
  • ca2cd9d4f5 a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone. aaron 2010-03-03 16:31:45 +0000
  • 790d2a7776 adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. aaron 2010-03-03 15:56:44 +0000
  • 0e9a6826b0 Update to VCF code to get it up to spec. ebanks 2010-03-03 06:12:42 +0000
  • 317fac8dff Better error message for --assume_single_sample_reads screw up ebanks 2010-03-03 01:03:10 +0000
  • 104f4f7383 Mediocre implementation of reader pooling within the SAM data source. Will fix this week. hanna 2010-03-02 22:35:02 +0000
  • 74a5223b11 oops - didn't mean to check this in ebanks 2010-03-02 20:28:22 +0000
  • 5f3c80d9aa 1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext. ebanks 2010-03-02 20:26:40 +0000
  • 6ceae22793 utility methods for genotype counts ebanks 2010-03-02 20:23:41 +0000
  • 7578678f99 refactored to provide a sum of mismatch quality scores capability as well (used by Cancer) kcibul 2010-03-02 16:40:03 +0000
  • 91b3f9745e removing the package description for the VCF validator aaron 2010-03-02 15:45:51 +0000
  • 232fcf829a removing the unsupported VCF validator aaron 2010-03-02 15:45:33 +0000
  • 1b572b192a Stopgap fix for temporary problems sharding when indexless. A more compelling solution will come later this week. hanna 2010-03-02 02:59:14 +0000
  • 75a541b479 Fix nasty issue where shard boundaries aren't properly clipped during locus traversals. hanna 2010-03-01 23:31:58 +0000
  • 9298e13201 Make annotated VCF not be broken andrewk 2010-03-01 23:22:41 +0000
  • af6e476df5 Copyright compliant rpoplin 2010-03-01 15:29:34 +0000
  • 3a863d3e8c Initial check in of VariantOptimizer in playground. There is a Gaussian Mixture Model version and a k-Nearest Neighbors version. There is still lots of work to do. Nobody should be using it yet. rpoplin 2010-03-01 15:26:18 +0000
  • 6133d73bf0 Locus (non-intervalled) traversal with new sharding system. hanna 2010-03-01 01:58:44 +0000
  • 80f5d2829d Support for read interval sharding with proper filtering. hanna 2010-02-27 20:26:34 +0000
  • d8fedd59be docs, cleanup, and some improvements to the iterators. aaron 2010-02-26 22:36:04 +0000
  • b69c2d0f70 Cleanup. Remove some unnecessary methods. hanna 2010-02-26 21:50:48 +0000
  • 30eb28886b Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so the mode of operation is currently queryOverlapping rather than queryContained. hanna 2010-02-26 21:41:55 +0000
  • cfff486338 This commit is for Kiran chartl 2010-02-26 18:18:38 +0000
  • 87f8fb7282 Quick commit in advance of Aaron's. Just a bunch of refactoring (private classes separated out, put in proper package). Also support added for coverage by read group rather than sample. chartl 2010-02-26 16:39:47 +0000
  • 622554d7bd disable a part of the ROD for Reads code until the rest of the system goes live aaron 2010-02-26 16:15:42 +0000
  • 496ecc8186 Change in how overall coverage and means are stored in the DOCS object; change from keeping track of sample mean coverage to keeping track of sample total coverage (calculate means at the end) chartl 2010-02-26 15:51:12 +0000
  • 1017a38f38 Initial refactoring of read traversal to make it easier to drop in intervalled reads traversal. hanna 2010-02-26 15:09:09 +0000
  • 9a6b384adb Support for no qual fields in VCF; better support for Mendelian violation calculations depristo 2010-02-26 00:29:17 +0000
  • 246fa28386 RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother. aaron 2010-02-25 22:48:55 +0000
  • 591102a841 Don't close the output stream if we're printing to stdout chartl 2010-02-25 21:50:58 +0000
  • 10cc71ceb0 Another midway commit for teh engineerz chartl 2010-02-25 21:24:02 +0000
  • 3289826892 Fix chartl's issue -- reduceInit() is sometimes called unnecessarily at the end of a traversal. hanna 2010-02-25 21:02:18 +0000
  • 3d92e5a737 Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt] chartl 2010-02-25 20:25:07 +0000
  • 553d39bb00 Clean up the code a bit following the introduction of reduceByInterval. hanna 2010-02-25 01:20:22 +0000
  • 199b43fcf2 Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a simplification of some of the locus traversal code. hanna 2010-02-25 00:16:50 +0000
  • 2572c24935 We were still dropping halves of some pairs, in which both reads were assigned to the same position. Fixed. asivache 2010-02-24 23:13:23 +0000
  • fef1154fc8 starting on RODs for Reads: made RODRecordList implement list<RODatum> (so we can sub in fake lists during testing), and removed unnecessary generic-ness. Removed BrokenRODSimulator, which isn't being used. aaron 2010-02-24 22:11:53 +0000
  • 9306041cf4 Since IntervalCleaner is gone for good, it is sensible to update the package to refer to the new IndelRealigner instead asivache 2010-02-24 16:42:56 +0000
  • 5df37968de Simplification of code segments; slight alteration to per-locus tabulation; added to-do items for cosmetic changes (mostly binning options and settigns) chartl 2010-02-24 05:20:18 +0000
  • 27d3ef9458 Got rid of annoying commented printouts; no functional changes asivache 2010-02-24 05:12:30 +0000
  • d73bc490c2 Do not build alt consensuses from insertions that have an N in the inserted sequence. Seems to cause problems rather than solve any asivache 2010-02-24 03:00:26 +0000
  • 94d74d4f78 Multiple instances of the same consensus were all living happily together in the set of alt consensuses. As the result, we have been taking considerable performance hit from trying to align all reads to those instances over and over again. Fixed. Only one copy of any given alt consensus is now stored. asivache 2010-02-24 02:09:50 +0000
  • 1f673e9fab Float the bins with the given lower bound chartl 2010-02-23 20:48:53 +0000
  • 119d449b46 Formatting changes chartl 2010-02-23 20:43:15 +0000
  • 173956927b Summaries generated for firehose from DoC output have been migrated to its own walker to calculate aggregate coverage statistics in a parallelizable and fast way. This is an initial commit, bug-fixing and testing is upcoming. chartl 2010-02-23 18:41:02 +0000
  • 491b30e8de Eliminate a few stray loci that weren't being filtered out. hanna 2010-02-23 18:00:52 +0000
  • fff15944fe Bug fix. Stopping condition of recurrence stopped too soon in some cases where an interval *contained* zero reads but *overlapped* with some reads. hanna 2010-02-23 15:58:54 +0000
  • 36129e01e4 Using bitmap() instead of png() since the former doesn't rely on X11. kshakir 2010-02-23 05:31:51 +0000
  • a0e8de40cf Bug fix: at one locus in the dataset, two reads were dropped. hanna 2010-02-22 23:54:52 +0000
  • 5546aa4416 adding code to deal with the off-spec situation where our minimum likelihood is above the GLF max of 255. aaron 2010-02-22 22:27:39 +0000
  • 88d0677379 Misc correctness enhancements: develop the bin selector into a recursive algorithm and return a shard when reads are missing. Also improve the performance of the read filter that clips reads not actually present in the shard. hanna 2010-02-22 22:19:06 +0000
  • 5f9c3f3884 Outputing annotated VCF to the current directory instead of attempting to write in the directory next to the original vcf. kshakir 2010-02-22 21:31:24 +0000
  • 8b555ff17c Killed the old cleaner code. Bye bye. ebanks 2010-02-22 20:49:58 +0000
  • 3738b76320 Added a playground concordance analyzer for summarizing VariantEval across a group. kshakir 2010-02-22 20:28:52 +0000
  • a640bd2d79 ignore uninteresting extended events ebanks 2010-02-22 19:55:46 +0000
  • 32e5dceef9 Moving comments. rpoplin 2010-02-22 19:27:31 +0000
  • b236714c8a Optimization - Added method to Covariates: void getValues( SAMRecord read, Comparable[] comparable ) which takes an array of size (at least) read.getReadLength() and fills it with covariate values for all positions in the given read. Made CovariateCounterWalker and TableRecalibrationWalker use this method instead of calling getValue(..) for each covariate and each offset. alecw 2010-02-22 17:35:25 +0000
  • 32d14d988e Overload parseIntervalRegion() to allow for the interval merging rule to be passed in (so one is not required to use the value from the GATK arg collection). Now the IndelRealigner can use this functionality without being forced to merge abutting intervals (which was actually causing a problem with the cleaning). ebanks 2010-02-22 04:13:54 +0000
  • cc09f48cd8 Correctness fix: index can concat chunks around shard edges, and my code didn't account for that. hanna 2010-02-19 21:44:33 +0000
  • 0e05a3acb0 Adding depth of coverage features to firehose summary tools chartl 2010-02-19 19:47:16 +0000
  • 71f18e941f Significant performance improvements made by subtracting out the contents of the prior highest-level bin. hanna 2010-02-19 16:46:16 +0000
  • 3e0e7aad2d Removing debug statement. oops. rpoplin 2010-02-19 15:26:22 +0000
  • 7f19ff1fa1 Added a new option in the recalibrator to be used by people who have SOLiD data in which only a few of the reads have no-calls in the color space. These reads will be skipped over and left in the bam file untouched. rpoplin 2010-02-19 15:25:23 +0000
  • b1a4e6d840 removing non-ascii characters from my Copyright and from VariantEval2Walker aaron 2010-02-18 18:54:36 +0000