class Minimap2::Aligner

• Minimap2::Aligner
• Reference
• Object

Overview

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

Defined in:

minimap2/aligner.cr

Constructors

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

  Shortcut constructor using common options.

• .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.

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

Class Method Summary

• .build : AlignerBuilder

  Create a new AlignerBuilder.

• .builder : AlignerBuilder

  DEPRECATED Use .build instead

• .cigar_op_char(op : UInt8) : Char

Instance Method Summary

• #finalize

  Release loaded minimap2 index parts.

• #idx_opt : LibMinimap2::MmIdxoptT
• #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.

• #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.

• #map_opt : LibMinimap2::MmMapoptT
• #n_seq : UInt32

  Number of reference sequences in the first loaded index part.

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

  Fetch a reference subsequence by contig name.

Constructor Detail

Class Method Detail

Instance Method Detail