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annotator
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Now, if a dbsnp rod is passed to either the UnifiedGenotyper or VariantAnnotator, a DB=0/1 annotation is added (in addition to filling in the ID field); this is in line with 1KG project calls. If no dbsnp rod is used, the annotation is not added (as opposed to setting every entry to DB=0).
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2010-01-25 17:27:12 +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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Optimizations:
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2009-12-16 21:39:58 +00:00 |
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fasta
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added changes to the code to allow different types of interval merging,
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2009-12-23 21:59:14 +00:00 |
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filters
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Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization.
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2009-12-18 19:16:41 +00:00 |
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genotyper
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Now, if a dbsnp rod is passed to either the UnifiedGenotyper or VariantAnnotator, a DB=0/1 annotation is added (in addition to filling in the ID field); this is in line with 1KG project calls. If no dbsnp rod is used, the annotation is not added (as opposed to setting every entry to DB=0).
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2010-01-25 17:27:12 +00:00 |
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indels
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Bug: ExpandedSAMRecord did not treat hard-clipped bases ('H') correctly. Fixed.
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2010-01-25 19:23:44 +00:00 |
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qc
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Made the VCF validator a simple rod walker instead of having it be in a separate package.
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2010-01-15 06:39:06 +00:00 |
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recalibration
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Fixing no platform warning message.
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2010-01-25 19:46:50 +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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In extended event lines, now prints deletions in verbose format as well (e.g. "-AAT")
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2009-12-30 21:57:20 +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 |
894a2b511b