add clip bypass options to rerun indexing without altering graphs#1899
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glennhickey merged 1 commit intomasterfrom Feb 23, 2026
Merged
add clip bypass options to rerun indexing without altering graphs#1899glennhickey merged 1 commit intomasterfrom
glennhickey merged 1 commit intomasterfrom
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cactus-graphmap-joincan't do anything without renormalizing and clipping the input graphs. This is annoying if, say, you just want to re-index or re-generate the vcfs.This pr adds some options,
--vgClip,--vgFilterand--vgFullto bypass these options. You pass in graphs output from previous runs via--chrom vg clip/filter/fulland it will take these graphs as / is for indexing/vcfing without running any other processing.In addition to the speedup, you get a guarantee that the resulting indexes are 100% compatible with the input files, since no graph edits are happening.
I'd be nice to have a way to just to vcf processing, but this is still better than nothing