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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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-baqGOP now takes phred scaled scores instead of probabilities in the command line.
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2011-01-13 00:06:38 +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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renaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation
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2010-10-08 14:08:28 +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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Make Indel Realigner exceptions related to not enough space on disk or a too low file-handle limit UserExceptions.
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2010-12-07 16:37:31 +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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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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genotype
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Moving GLF code to archive
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2011-01-15 22:42:42 +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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Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.
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2011-01-07 22:03:36 +00:00 |
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pileup
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Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.
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2011-01-20 12:54:03 +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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Fix Picard OTF index generation issue.
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2011-01-26 03:42:46 +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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A significant refactoring of the ROD system, done largely to simplify the process of
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2010-12-31 04:52:22 +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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Added validator for phasing using read information, e.g., PacBio: ReadBasedPhasingValidationWalker
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2011-01-05 20:05:56 +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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Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.
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2011-01-20 12:54:03 +00:00 |
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GenomeLocParser.java
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Looking over the daily error log email made me realize that there were 2 implementations of vc.modifyLocation() - the correct one in VC that didn't require lazy loading the genotype data and the bad one in VCUtils that did. Removing the implementation in VCUtils and updating the code accordingly. Also, removing createPotentiallyInvalidGenomeLoc() since no one uses it anymore.
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2010-11-26 18:40:34 +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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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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MathUtils.java
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Better documentation
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2011-01-23 03:36:09 +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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Checking in everyone's changes to the variant recalibrator. We now calculate the variant quality score as a LOD score between the true and false hypothesis. Allele Count prior is changed to be (1 - 0.5^ac). Known prior breaks out HapMap sites
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2010-08-05 14:12:19 +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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SW-turbo. Kind of. This implementation is presumably equivalent to the old one (mathematically), but runs ~10 times faster: inner loops eliminated completely. The author of the original implementation should be sentenced to the galleys. Oh, that would be me...
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2010-12-01 00:08:47 +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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For the fullCallingPipeline.q:
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2011-01-20 22:34:43 +00:00 |
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WilcoxonRankSum.java
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Fix for NaNs in the rank sum tests.
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2011-01-05 15:21:30 +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 |
f29bb0639b