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datasources
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Display a more intelligent error message if the user runs a locus traversal across an unmapped reads file.
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2009-07-14 18:36:09 +00:00 |
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examples
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First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.
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2009-06-30 21:59:54 +00:00 |
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executive
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Warning for possibly mismatched reads / reference was very aggressive. Relax
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2009-07-14 16:21:22 +00:00 |
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filters
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Until 454 goes far, far away, at least we can completely ignore it
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2009-07-10 18:31:53 +00:00 |
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iterators
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Some quick and dirty fixes to support querying unmapped BAM files.
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2009-07-14 01:25:20 +00:00 |
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refdata
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Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant
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2009-07-14 18:53:27 +00:00 |
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traversals
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a small refactoring, and some documentation cleanup
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2009-07-09 22:03:45 +00:00 |
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walkers
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The number of loci can easily overflow an int. Change reduce type to a Long.
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2009-07-14 16:07:00 +00:00 |
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CommandLineExecutable.java
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Fix for GSA-90: GATK banner and error messages should point to the wiki website.
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2009-07-13 21:56:41 +00:00 |
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CommandLineGATK.java
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Fix for GSA-90: GATK banner and error messages should point to the wiki website.
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2009-07-13 21:56:41 +00:00 |
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GATKArgumentCollection.java
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Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.
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2009-07-08 20:26:16 +00:00 |
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GenomeAnalysisEngine.java
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Oops! Accidentally deactivated the ArgumentFactory, needed by the CleanedReadInjector, while refactoring last night.
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2009-07-13 16:41:55 +00:00 |
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LocusContext.java
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Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
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2009-06-30 19:17:24 +00:00 |
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OutputTracker.java
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Lazy creation of output streams. Only create output streams when absolutely necessary.
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2009-05-26 21:56:57 +00:00 |
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Reads.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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WalkerManager.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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package.html
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More package-level documentation.
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2009-06-17 16:28:45 +00:00 |
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