Make vg inject use AlignmentEmitter and support GAF #4319
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Changelog Entry
To be copied to the draft changelog by merger:
vg injectnow supports GAF format with the new--output-format/-ooptionDescription
This makes
vg injectuse the AlignmentEmitter instead of directly using Protobuf emitter stuff.This means it should get all the fancy GAM block interleaving stuff we do for speed in the mappers. I noticed the existing implementation wasn't able to consistently keep 16 threads busy; it would run all the threads for a while, and then drain, and then do it again. I haven't tested if this actually solves that problem, but it should eliminate one potential cause. Also it gives us essentially free GAF support.