vg inject now supports GAF format with the new --output-format/-o option
Description
This makes vg inject use 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.
Changelog Entry
To be copied to the draft changelog by merger:
vg inject
now supports GAF format with the new--output-format
/-o
optionDescription
This makes
vg inject
use 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.