class

Minimap2::Aligner

Inherits Reference < Object

High-level Aligner convenience class

Constructors

from_strings(seqs : Array(String), names : Array(String) | Nil = nil, preset : String | Nil = nil) : Aligner

Build an Aligner from sequence strings.

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new(idx_opt : MmIdxOpt, map_opt : MmMapOpt, indices : Array(MmIdx))
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Class methods

from_file(fn : String, preset : String | Nil = nil, n_threads : Int32 = 1) : Aligner | Nil

Build an Aligner from a FASTA/FASTQ file.

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Instance methods

idx_opt
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indices
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map(seq : String, qname : String | Nil = nil, & : MmReg1 -> Nil) : Nil

Map a query string; yields MmReg1 hits.

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map(seq : String, qname : String | Nil = nil) : Array(MmReg1)

Map a query string; returns Array of hits.

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map_opt
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seq_lengths

Return the index sequence lengths.

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seq_names

Return the index sequences.

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