class

Minimap2::Aligner

Inherits Reference < Object

High-level aligner API backed by minimap2 index and mapping routines.

Constructors

new(path : String, preset : String | Nil = nil, threads : Int32 = 1, output : String | Nil = nil, cigar : Bool = false)

Shortcut constructor using common options.

Prefer Aligner.build for explicit configuration chains.

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new(path : String, preset : String | Nil = nil, threads : Int32 = 1, output : String | Nil = nil, cigar : Bool = false, &block : AlignerBuilder -> )

Shortcut constructor with additional builder customization block.

Keyword options are applied before yielding the builder.

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new(idxopt : LibMinimap2::MmIdxoptT, mapopt : LibMinimap2::MmMapoptT, threads : Int32, path : String, output : String | Nil)
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Class methods

build

Create a new AlignerBuilder.

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builder

DEPRECATED Use .build instead

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cigar_op_char(op : UInt8) : Char
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Instance methods

finalize

Release loaded minimap2 index parts.

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idx_opt
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map(seq : String, cs : Bool = false, md : Bool = false, ds : Bool = false, max_frag_len : Int32 | Nil = nil, extra_flags : Array(UInt64) | Nil = nil, query_name : String | Nil = nil) : Array(Mapping)

Map a query string against the loaded index.

Set cs, md, ds to include optional alignment tag strings.

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map(seq : Bytes, cs : Bool = false, md : Bool = false, ds : Bool = false, max_frag_len : Int32 | Nil = nil, extra_flags : Array(UInt64) | Nil = nil, query_name : String | Nil = nil) : Array(Mapping)

Map a query byte slice against the loaded index.

extra_flags accepts raw minimap2 flag constants from LibMinimap2.

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map_opt
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n_seq

Number of reference sequences in the first loaded index part.

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seq(name : String, start : Int32 = 0, stop : Int32 = Int32::MAX) : String | Nil

Fetch a reference subsequence by contig name.

Coordinates are 0-based, half-open (start...stop).

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