class

Minimap2::AlignerBuilder

Inherits Reference < Object

Builder for creating a Minimap2::Aligner with preset and mapping options.

Constants

PRESETS = { map_ont: "map-ont", map_hifi: "map-hifi", map_pb: "map-pb", splice: "splice", splice_hq: "splice:hq", splice_sr: "splice:sr", asm5: "asm5", asm10: "asm10", asm20: "asm20", sr: "sr", }

Preset shortcuts mapped to minimap2 preset strings.

Constructors

Instance methods

asm10
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asm20
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asm5
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map_hifi
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map_ont
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map_pb
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preset(preset : String) : self

Apply a minimap2 preset string (e.g. "map-ont", "map-hifi", "splice").

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splice
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splice_hq
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splice_sr
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with_cigar

Enable CIGAR generation and cs-tag output for mapped records.

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with_index(path : String, output : String | Nil = nil) : Aligner

Build an aligner from a reference FASTA/MMI path.

If output is provided, a built index is written to that path.

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with_index_threads(threads : Int32) : self

Set the number of threads used while building/loading the index.

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