module Minimap2
Defined in:
minimap2.crminimap2/aligner.cr
minimap2/builder.cr
minimap2/ffi.cr
minimap2/seq_util.cr
minimap2/types.cr
Constant Summary
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VERSION =
{{ (`shards version /home/runner/work/minimap2-cr/minimap2-cr/src`).chomp.stringify }}
Class Method Summary
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.fetch_seq(idx : Pointer(LibMinimap2::MmIdxT), name : String, start : Int32 = 0, stop : Int32 = Int32::MAX) : String | Nil
Fetch a subsequence from an index by contig name.
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.idx_seq(seq : String, w : Int32, k : Int32, is_hpc : Bool = false, bucket_bits : Int32 = 14) : Pointer(LibMinimap2::MmIdxT)
Build an in-memory index from a single sequence.
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.revcomp(seq : String) : String
Utilities adapted from minimap2 mappy helpers.
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.revcomp(seq : Bytes) : String
Returns the reverse-complement of a sequence byte slice.
Class Method Detail
def self.fetch_seq(idx : Pointer(LibMinimap2::MmIdxT), name : String, start : Int32 = 0, stop : Int32 = Int32::MAX) : String | Nil
#
Fetch a subsequence from an index by contig name.
Coordinates are 0-based, half-open (start...stop).
def self.idx_seq(seq : String, w : Int32, k : Int32, is_hpc : Bool = false, bucket_bits : Int32 = 14) : Pointer(LibMinimap2::MmIdxT)
#
Build an in-memory index from a single sequence.
Useful for tests and small ad-hoc alignment tasks.
def self.revcomp(seq : String) : String
#
Utilities adapted from minimap2 mappy helpers.
Returns the reverse-complement of a DNA/RNA sequence string.