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analysis
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Initial commit of items for analyzing amino acid transitions in variant eval. Blew up my subversion by coding locally while i did not have internet. I hope this doesn't bust any integrationtests since I changed no existing code but...who knows. Crossing my fingers.
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2010-06-29 20:57:18 +00:00 |
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baq
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Removed MAG entirely
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2011-03-18 19:43:23 +00:00 |
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bed
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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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classloader
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Stamp out lazy loading in the PluginManager. This is an attempt to stamp
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2011-01-13 20:58:28 +00:00 |
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collections
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A version of VQSRv2 that does contrastive clustering in two passes. The walkers will be renamed when they are moved to core.
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2011-03-14 21:03:56 +00:00 |
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duplicates
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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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exceptions
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A nicer error (UserException now) for malformed genome locs
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2011-03-18 02:58:29 +00:00 |
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fasta
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Update Picard / sam-jdk at Tim's request.
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2011-01-03 02:17:25 +00:00 |
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file
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Removing stray non-ASCII character
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2011-02-02 03:10:08 +00:00 |
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genotype
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Initial commit of new likelihood model to evaluate indel quality. Principle is simple, a plain Pair HMM with affine gap penalties (in log space) that does quasi-local alignment between reads and candidate haplotypes and which in theory should be more solid and more reliable than the older Dindel-based model. It also allows to be easily extensible in the future if we decide to introduce either context-dependent and/or read-dependent gap penalties.
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2011-03-07 15:31:58 +00:00 |
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help
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Excluding the QFunction log files from the set of files to delete on completion.
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2010-11-18 20:22:01 +00:00 |
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instrumentation
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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interval
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A few minor modifications masquerading as significant changes according to
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2011-02-03 17:59:19 +00:00 |
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pileup
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Renamed StratifyAlignmentContext to AlignmentContextUtils, and StatiefyContextType to ReadOrientation. Also, went through the system and deleted all references to second bases. That ship passed long ago. This was the actual commit, the last was an intellij error
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2011-04-03 15:36:17 +00:00 |
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report
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Recent changes to the build system make the build system complain loudly about
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2010-09-24 22:09:12 +00:00 |
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sam
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Added support for a general GATK option --simplifyBAM to automatically remove and simplify kept reads in an output BAM file. Specifically, duplicate, non-PF, and unmapped reads are removed, and all extended tags in the retained SAM records are removed except the RG:Z tag. This option is very useful when creating temporary BAM files (merged per-population or multi-sample cleaned) for future calling (as in the 1000G processing pipeline). Results in a significant reduction in space of the resulting BAM, faster reading of the BAM, and surprisingly even faster UG performance:
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2011-03-26 01:21:35 +00:00 |
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text
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GenotypeConcordance now prints interesting sites more nicely. RMDTrackBuilder is now uses the root class FeatureSource not BasicFeatureSource.
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2010-10-20 00:29:02 +00:00 |
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threading
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Documentation and cleanup of the distributed GATK implementation. Detailed documentation -- given that Matt will be extending the system in the near future -- about how the locking and processing trackers work. Added error trapping to note that distributed, shared-memory parallelism isn't yet implemented, instead of just not working silently. General utility function for the analysis of distributedGATK operation in the analysis directory
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2011-01-28 03:40:09 +00:00 |
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vcf
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In the process of optimizing ProduceBeagleInputWalker, discovered that the GenotypeLikelihoods, the UG, and Genotype objects were using old-style GL tags internally, and then converting from Likelihoods -> GL String -> Likelihoods -> PL String throughout the GATK. It was both painful and led to convoluted code throughout the system. Removed everything but GL conversion -> PL in the GenotypeLikelihoods objects, and now all of the codes in UG now immediately provides GenotypeLikelihoods to the Genotype objects, which is converted straight to PL now. Resulted in a 30% speed up in ProduceBeagleLikelihoods, passes integration tests without any modifications, and likely speeds up writing any VCFs with likelihoods.
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2011-03-13 00:07:51 +00:00 |
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wiggle
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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yaml
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Updated from SnakeYAML 1.6 to 1.7.
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2010-09-22 19:47:49 +00:00 |
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BaseUtils.java
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Renamed StratifyAlignmentContext to AlignmentContextUtils, and StatiefyContextType to ReadOrientation. Also, went through the system and deleted all references to second bases. That ship passed long ago. This was the actual commit, the last was an intellij error
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2011-04-03 15:36:17 +00:00 |
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CardinalityCounter.java
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Moved phasing-specific utilities to phasing sub-directory
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2011-01-13 15:38:20 +00:00 |
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DisjointSet.java
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Moved phasing-specific utilities to phasing sub-directory
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2011-01-13 15:38:20 +00:00 |
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GenomeLoc.java
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Failed to include some required GenomeLoc utilities in my last commit.
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2011-03-07 23:00:17 +00:00 |
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GenomeLocParser.java
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A nicer error (UserException now) for malformed genome locs
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2011-03-18 02:58:29 +00:00 |
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GenomeLocSortedSet.java
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vastly improved progress meter that estimates % of work done and time until the job finishes and time remaining. Reordered GATK core initialization order -- intervals are created before the scheduler.
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2011-01-12 17:32:27 +00:00 |
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HasGenomeLocation.java
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Incremental commit for distributed computation. Appears to work but has potential deadlock situation not yet debugged. Do not use yet.
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2011-01-17 21:23:09 +00:00 |
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HeapSizeMonitor.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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IndelUtils.java
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GenotypeAndValidate: now looks at annotations in the INFO field instead of filter field. Better output and filters repetitive calls to indel extended events.
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2011-03-15 21:54:40 +00:00 |
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MalformedGenomeLocException.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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MannWhitneyU.java
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Minor changes to MannWhitneyU:
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2011-03-30 17:03:02 +00:00 |
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MathUtils.java
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Whitespace cleanup
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2011-03-17 18:04:08 +00:00 |
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MendelianViolation.java
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SelectVariants: now keeps the YAML stuff internal... it's there if you wanna use it, but won't be published anymore. Official parameter is the string for now.
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2011-03-15 18:36:55 +00:00 |
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PathUtils.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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PreciseNonNegativeDouble.java
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Moved phasing-specific utilities to phasing sub-directory
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2011-01-13 15:38:20 +00:00 |
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QualityUtils.java
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Renamed StratifyAlignmentContext to AlignmentContextUtils, and StatiefyContextType to ReadOrientation. Also, went through the system and deleted all references to second bases. That ship passed long ago. This was the actual commit, the last was an intellij error
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2011-04-03 15:36:17 +00:00 |
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ReservoirDownsampler.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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SWPairwiseAlignment.java
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Get rid of score cutoff at 0 in the alignment matrix (i.e. score[cell] = max(0, score[from_parent_cells]). Use the computed score as is. Technically, it's pretty much NW now, not SW.
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2011-04-01 00:11:04 +00:00 |
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SampleUtils.java
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A more general method for specifying samples to act on from the command-line. Supports samples specified individually on the console, a file of samples, or regular expressions to select multiple samples.
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2011-01-06 14:54:56 +00:00 |
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SequenceDictionaryUtils.java
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- Fix DepthOfCoverage so that, when it abuses the ROD system by instantiating a track in onTraversalDone, it also supplies the correct sequence dictionary and parser.
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2010-11-15 20:34:04 +00:00 |
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SimpleTimer.java
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Bug fix for SimpleTimer that didn't always convert elapsed times from milliseconds to seconds
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2011-01-22 18:50:59 +00:00 |
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Utils.java
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Enabled the parameterize option for debugging PipelineTest MD5s.
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2011-03-26 00:41:47 +00:00 |
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WilcoxonRankSum.java
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Adding ReadPos rank sum test. Transitioned rank sum tests over to using Chris's implementation in order to harmonize the codebase. There isn't any reason to have competing implementations of rank sum. Thanks to Chris for adding the necessary hypothesis testing options. WilcoxonRankSum.java will be deleted soon.
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2011-04-02 22:26:35 +00:00 |
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package-info.java
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
b316c9a590