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annotator
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In retrospect, it wasn't a good idea to have FisherStrand handle reduced reads since they are always on the forward strand. For now, FS ignores reduced reads but I've added a note (and JIRA) to make this work once the RR het compression is enabled (since we will have directionality in reads then).
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2012-12-05 02:00:35 -05:00 |
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beagle
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FindBugs 'Efficiency' fixes
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2012-08-16 15:40:52 -04:00 |
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bqsr
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Merged bug fix from Stable into Unstable
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2012-11-25 21:55:55 -05:00 |
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compression/reducereads
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Co-Reduction implementation in ReduceReads
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2012-11-14 10:33:21 -05:00 |
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coverage
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Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)
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2012-11-21 15:56:53 -05:00 |
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diagnostics
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Bugfix for GSA-647 HaplotypeCaller misses good variant because the active region doesn't trigger for an exome
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2012-11-01 15:34:04 -04:00 |
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diffengine
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Tests didn't like my note to Geraldine in the output logs; apparently it's tested in integration tests
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2012-11-27 14:40:49 -05:00 |
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fasta
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Update docs
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2012-11-27 08:24:41 -05:00 |
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filters
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Adding extraDocs tag per Mauricio's request
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2012-07-25 18:23:18 -04:00 |
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genotyper
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Fix for GSA-615: UnifiedGenotyperEngine.getGLModelsToUse takes 5% of the runtime of UG, should be optimized away.
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2012-12-12 20:25:45 +00:00 |
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indels
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Bug fix for indel HMM: protect against situation where long reads (e.g. Sanger) in a pileup can lead to a read starting after the haplotype end for a given haplotype.
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2012-12-09 02:09:34 -05:00 |
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phasing
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Fix for PBT bug reported on the forum: the AD is actually output correctly now (rather than with 'null' or some gibberish memory pointer).
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2012-12-13 23:28:30 +00:00 |
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qc
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ReduceReads is now scattered by contig
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2012-12-10 15:25:27 -05:00 |
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validation
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Fix GenotypeAndValidate to handle SNPs and indels as reported on the forum. Recent changes to the UnifiedArgumentCollection made this stop working. Adding in JIRA to create integration tests for this tool.
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2012-10-25 10:06:13 -04:00 |
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varianteval
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Merged bug fix from Stable into Unstable
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2012-11-27 10:27:08 -05:00 |
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variantrecalibration
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introduce a level of indirection for the forum URLs - this new function will allow me a place to morph the URL into something that is supported by Confluence
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2012-12-03 22:33:02 -05:00 |
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variantutils
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Continue to fix the case where PRIORITIZE is used but no priority list is given. While fixing that case I also removed unnecessary sorting, when the prioeity list is not provied. When the priority list is not provided, it will continue to be null. Thus, the number of original Variant Contexts should be given as a new parameter to simpleMerge (since priority might be null). This new parameter is used for checking if there are filtered VC, when annotationOrigin is true.
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2012-12-10 22:23:58 -05:00 |
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ActiveRegionExtension.java
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Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.
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2012-04-17 14:22:48 -04:00 |
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ActiveRegionWalker.java
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Add ActiveRegionReadState handling
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2012-11-28 13:59:57 -05:00 |
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Allows.java
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Removed support for RMD in @Requires and @Allows
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2011-08-03 15:36:55 -04:00 |
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Attribution.java
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…
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BAQMode.java
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General infrastructure for ReadTransformers
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2012-08-31 13:42:41 -04:00 |
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By.java
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…
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ClipReads.java
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Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers
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2012-08-30 10:15:10 -04:00 |
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DataSource.java
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Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.
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2012-08-17 14:55:38 -04:00 |
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Downsample.java
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Downsampling: experimental engine integration
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2012-09-06 15:03:27 -04:00 |
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DuplicateWalker.java
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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FlagStat.java
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GSA-515 Nanoscheduler GSA-550 ThreadSafeMapReduce shouldn't be super interface of TreeReducible
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2012-09-05 17:37:56 -04:00 |
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LocusWalker.java
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Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.
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2012-08-17 14:55:38 -04:00 |
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Multiplex.java
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…
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Multiplexer.java
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…
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NanoSchedulable.java
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Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"
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2012-09-10 15:52:39 -04:00 |
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PartitionBy.java
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…
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PartitionType.java
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Better default partition types for walkers
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2011-11-01 19:47:10 -04:00 |
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Pileup.java
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GSA-515 Nanoscheduler GSA-550 ThreadSafeMapReduce shouldn't be super interface of TreeReducible
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2012-09-05 17:37:56 -04:00 |
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PrintRODs.java
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Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers.
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2012-07-25 21:40:28 -04:00 |
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PrintReads.java
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GSA-515 Nanoscheduler GSA-550 ThreadSafeMapReduce shouldn't be super interface of TreeReducible
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2012-09-05 17:37:56 -04:00 |
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RMD.java
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…
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ReadFilters.java
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gatkdoc now generalized to use @Annotation. Multiple subsystems now use annotation to receive docs
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2011-07-23 20:00:35 -04:00 |
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ReadPairWalker.java
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…
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ReadWalker.java
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Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers
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2012-08-30 10:15:10 -04:00 |
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RefWalker.java
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Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.
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2012-08-17 14:55:38 -04:00 |
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Reference.java
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…
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RemoveProgramRecords.java
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Add a RemoveProgramRecords annotation
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2012-08-03 09:54:16 -04:00 |
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Requires.java
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…
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RodWalker.java
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…
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SplitSamFile.java
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Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers
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2012-08-30 10:15:10 -04:00 |
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TreeReducible.java
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GSA-515 Nanoscheduler GSA-550 ThreadSafeMapReduce shouldn't be super interface of TreeReducible
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2012-09-05 17:37:56 -04:00 |
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Walker.java
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General infrastructure for ReadTransformers
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2012-08-31 13:42:41 -04:00 |
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WalkerName.java
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…
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Window.java
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…
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package-info.java
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696bf95fba