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Add -x hifi preset for PacBio HiFi genomic DNA - #30
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-x hifi (alias map-hifi) is the dna preset plus one output-stage step: stretches of fragmented long gaps are realigned under map-hifi scoring, so one SV is not split into several false deletions. Placement, MAPQ and filtering are unchanged from dna. Preset names now ignore case, and ont is an alias for dna (dna output unchanged). Validation: docs/validation/2026-10-28-hifi/ Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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-x hifi(aliasmap-hifi) for PacBio HiFi genomic DNA, andontas an alias fordna. Preset names now ignore case.-x hifiis thednapreset plus one step at output: stretches of fragmented long gaps are realigned under minimap2map-hifiscoring, so one SV isn't split into several false deletions. Placement, MAPQ and filtering are the same asdna, and it usesdnaindexes.dnaoutput is unchanged.HG002 whole genome, against minimap2
map-hifi:Report:
docs/validation/2026-10-28-hifi/. Iso-Seq/Kinnex RNA hasn't been tested yet.