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--activeRegionIn argument nonfunctional
I've been trying to do some manual adjustments of active regions by running HaplotypeCaller with the --justDetermineActiveRegions option, reading in and adjusting the active region output, and then rerunning HaplotypeCaller with the --activeRegionIn option.
GATK completely ignores the input ARs and produces completely identical results regardless of what active regions I provide. Inspection of the --debug output shows that the same active regions are used as originally produced.
Some source diving has shown that the input active regions are read in in the walker initialize() function, while active region identification is done in the traverser. The traverser inspects the walker to see if input regions are available, and if not, runs the standard AR identification algorithm. Unfortunately, that inspection is done only once, during the traverser initialize(), and cached for later use. In the engine execution, the traverser is initialized before the walker, and so the uninitialized walker is queried for active regions, leading to a complete drop of any input data.