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annotator
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Two new annotations:
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2010-01-29 23:23:00 +00:00 |
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concordance
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Added a walker to the vcf tools compilation: one that combines vcf records. Both merges and unions are supported (see documentation... when it gets written this week).
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2010-01-10 06:45:11 +00:00 |
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coverage
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Fix for overflow issues
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2010-01-27 13:37:16 +00:00 |
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fasta
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Ups, I did it again. Fixing the bug introduced in a previous commit: use correct length of the indel event.
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2010-01-27 21:51:54 +00:00 |
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filters
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VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful
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2010-01-29 12:13:08 +00:00 |
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genotyper
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The UG calculations are now driven by an independent engine.
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2010-02-01 20:57:31 +00:00 |
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indels
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More plumbing: if after the shift window contains indel(s) at the first position, do not throw an exception, just print the warning (we can not deal with this situation!!) and discard those indels without trying to call them. This situation will most probably arise after forced shift over a messy region anyway.
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2010-02-04 21:06:28 +00:00 |
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qc
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1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files.
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2010-02-04 04:12:49 +00:00 |
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recalibration
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Added -name argument to AnalyzeAnnotations that allows one to specify the name of the annotation to be used on the plots. Instead of seeing AB and DP, one can add -name AB,AlleleBalance -name DP,Depth
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2010-01-29 20:48:53 +00:00 |
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varianteval
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Moved VariantEval to core. Updated integration test md5s to reflect new Analysis class names.
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2010-02-02 00:22:15 +00:00 |
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Allows.java
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@Required / @Allows flags for main arguments.
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2009-05-19 23:26:17 +00:00 |
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By.java
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Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
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2009-05-15 21:02:12 +00:00 |
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ClipReadsWalker.java
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Enhance the I/O management system to support custom headers and set the presorted flag
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2010-01-12 18:21:42 +00:00 |
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DataSource.java
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Framework for ROD walkers -- totally experiment and not working right now
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2009-09-12 19:13:15 +00:00 |
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DuplicateWalker.java
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Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker
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2009-12-29 19:46:29 +00:00 |
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FixBAMSortOrderTag.java
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More documentation for walkers that I'm familiar with in the collection of core walkers.
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2009-12-11 18:02:33 +00:00 |
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FlagStatWalker.java
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More documentation for walkers that I'm familiar with in the collection of core walkers.
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2009-12-11 18:02:33 +00:00 |
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LocusWalker.java
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Cleaned division of responsibilities between arguments to map function. Reference has been changed
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2009-08-04 21:01:37 +00:00 |
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LocusWindowWalker.java
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ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance
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2009-11-25 20:54:44 +00:00 |
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PileupWalker.java
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Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface.
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2010-01-26 13:53:29 +00:00 |
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PrintRODsWalker.java
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More documentation for walkers that I'm familiar with in the collection of core walkers.
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2009-12-11 18:02:33 +00:00 |
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PrintReadsWalker.java
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More documentation for walkers that I'm familiar with in the collection of core walkers.
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2009-12-11 18:02:33 +00:00 |
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RMD.java
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Windowed access to the reference.
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2009-08-05 16:29:15 +00:00 |
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ReadFilters.java
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Better support for specifying read filters to apply directly from the walkers.
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2009-07-09 23:59:53 +00:00 |
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ReadWalker.java
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Cleaned division of responsibilities between arguments to map function. Reference has been changed
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2009-08-04 21:01:37 +00:00 |
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RefWalker.java
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Added REFERENCE_BASES required annotation for performance
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2009-06-18 21:03:57 +00:00 |
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Reference.java
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Windowed access to the reference.
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2009-08-05 16:29:15 +00:00 |
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Requires.java
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@Required / @Allows flags for main arguments.
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2009-05-19 23:26:17 +00:00 |
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RodWalker.java
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Framework for ROD walkers -- totally experiment and not working right now
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2009-09-12 19:13:15 +00:00 |
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SplitSamFileWalker.java
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More documentation for walkers that I'm familiar with in the collection of core walkers.
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2009-12-11 18:02:33 +00:00 |
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TreeReducible.java
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N-way parallelism. Works for small test cases. Untested for large test cases.
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2009-05-01 19:34:09 +00:00 |
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Walker.java
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Reads now have new traversal flag: generateExtendedEvents(). Support added to GenomeAnalysisEngine and Walker. This is a silent and transparent framework change that no existing code is going to see. The actual code that makes use of the new flag (which is false by default) will be committed separately...
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2009-12-28 19:52:44 +00:00 |
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WalkerName.java
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Make command-line arguments available in walker constructor, provide back door from
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2009-03-26 20:45:27 +00:00 |
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Window.java
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Windowed access to the reference.
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2009-08-05 16:29:15 +00:00 |
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package-info.java
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Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file
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2009-12-04 20:08:41 +00:00 |
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