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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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More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated
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2011-03-03 03:55:24 +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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Fixed exception for BAMs without filenames (unit tests, BAM input streaming,
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2011-03-06 13:43:49 +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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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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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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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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More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated
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2011-03-03 03:55:24 +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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CalculateChromosomeCounts() now only calculates AC, AF, and AN when there are genotypes. Can now combine variants with headers that differ in only whether a field is a integer or a float. Updated CombineVariants integrationtest, as incorrect AC values where being calculated in the previous GS outputs.
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2011-03-06 19:25:52 +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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IndelUtils.java
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Fixes and cleanups for indel eval module. Also outputs AT/CG ratio in dedicated column in IndelStatistics.
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2011-02-28 12:07:50 +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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Added a boatload of new case-control association modules. Switched the U-test to use longs rather than ints (it just so happened that I overflowed and started getting negative U statistics. Not good.) Added the ALL association type for ease of specifying that we want to throw the book at something. Added an svn-commit.tmp~ because i can't get rid of it even with --force. Hopefully I can remove it after.
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2011-03-06 21:58:12 +00:00 |
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MathUtils.java
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A trivial, but useful, sum of a list of integers
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2011-03-05 06:09:05 +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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Subtle but very annoying bug due to incorrect exit condition on backward traversal. Example of incorrect old behavior (found by Martha Borkan, this normally would NOT happen with the combination of match/mismatch/open/extend parameters we have been using; use match=10.0, mismatch= -9.0, open= -15.0, extend= -6.66 in older builds in order to reproduce):
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2011-02-17 00:02:32 +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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Trivial header cleanup
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2011-02-04 22:23:15 +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 |
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