9d69bd2c84
@CoverageAndPowerWalker - removed a hanging colon that was being printed after the reference position @VariantEvalWalker - added a command line argument for pool size for eventual use in doing pooled caller evaluations. As now, the variable is unused. @AlignmentContext - altered the scope of class variables from private to protected in order that child objects might have access to them New Additions: Filtered Contexts Sometimes we want to filter or partition reads by some aspect (quality score, read direction, current base, whatever) and use only those reads as part of the alignment context. Prior to this I've been doing the split externally and creating a new AlignmentContext object. This new approach makes it a bit easier, as each of these objects are children of AlignmentContext, and can be instantiated from a "raw" AlignmentContext. @FilteredAlignmentContext is an abstract class that defines the behavior. The abstract method 'filter' is called on the input AlignmentContext, filtering those reads and offsets by whatever you can think of. The filtered reads/offsets are then maintained in the reads and offsets fields. These classes can be passed around as AlignmentContexts themselves. Writing a new kind of read-filtered alignment context boils down to implementing the filter method. @ReverseReadsContext - a FilteredAlignmentContext that takes only reads in the reverse direction @ForwardReadsContext - a FilteredAlignmentContext that takes only reads in the forward direction @QualityScoreThresholdContext - a FilteredAlignmentContext that takes only reads above a given quality score threshold (defaults to 22 if none provided). A unit test bamfile and associated unit tests for these are in the works. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1559 348d0f76-0448-11de-a6fe-93d51630548a |
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