a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
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more like a resource bundle at this point, changed it over to use the Java ResourceBundle
support classes.
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below the specific command-line arguments for the walker. Also introduced
@help.summary to override summary descriptions if required.
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and displays walker data extracted from the JavaDoc. Needs a bit of help,
both in content and flexibility of package naming.
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inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
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the pathway from command line to traversal engine.
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walker into GATK itself, do some cleanup of output messages, and add some bug fixes.
Command-line arguments in walkers are now feature-complete, but still a bit messy.
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(yet) deal elegantly with even simple cases.
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hanna
aaron
depristo