class Minimap2::AlignerBuilder

• Minimap2::AlignerBuilder
• Reference
• Object

Overview

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

Defined in:

minimap2/builder.cr

Constant Summary

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

• .new

Instance Method Summary

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

  Apply a minimap2 preset string (e.g.

• #splice : self
• #splice_hq : self
• #splice_sr : self
• #sr : self
• #with_cigar : self

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

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

  Build an aligner from a reference FASTA/MMI path.

• #with_index_threads(threads : Int32) : self

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

Constructor Detail

Instance Method Detail