fix --mgSplitWholeGenomeRef option bug - #2011
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glennhickey wants to merge 2 commits into
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9b0ce2d passed name= and cores= to merge_pafs_sized, but toil's FunctionWrappingJob pops memory/cores/disk/accelerators/preemptible/checkpoint/ name out of the kwargs before calling the function, using "name" as the job's unitName. Both were swallowed: the merged file kept the default 'merged.paf' for the GAF merge too, and the bgzip ran on one thread, which is what that commit was meant to fix. Rename them merged_name and gzip_cores; gzip_cores is still passed on to the child as cores=, where toil eating it is the point. Visible in an HPRC log as jobs literally named "merged.gaf" and "merged.paf" either side of `bgzip .../merged.paf --threads 1`. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XScUpHRSBsui9Y67uQxA6a
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Fix issue where second reference wouldn't get chromosome binned like everything else, allowing for bits of it to bleed into different chromsomes. Only an issue in the new
--mgSplitWholeGenomeoption. The reason was that all references would appear full-genome in every chromosome. But only the first reference is properly post-processed out.This patch takes the simple and easy fix: just use the first reference whole-genome. Since the whole point is better mapq, it should be fine (and even a bit faster).
Caught this because the bug resulted in invalid rGFA, with different ranks getting applied to different segments of the same contig.