Unified parallel GBWT construction #4221
Merged
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Changelog Entry
To be copied to the draft changelog by merger:
Description
This PR updates GBWTGraph to include unified support for multithreaded GBWT construction (see jltsiren/gbwtgraph#36). The main idea is to partition the graph into GBWT construction jobs using
gbwt_construction_jobs()
, create the final metadata withMetadataBuilder
, pass reference paths withassign_paths()
andinsert_paths()
, build partial GBWTs for the jobs in parallel, merge the GBWTs, and add metadata fromMetadataBuilder
.vg gbwt
andvg autoindex
. As a byproduct, we get parallelization for them.vg haplotypes
uses this to the extent possible.rebuild_gbwt()
still uses the old parallelization scheme, as it's built into the interface.