minimap2 0.2.31.0 → 1.2.31.0

data/lib/minimap2/ffi/mappy.rb

@@ -1,104 +0,0 @@
-# frozen_string_literal: true
-
-# https://github.com/lh3/minimap2/blob/master/python/cmappy.h
-
-module Minimap2
-  module FFI
-    class Hit < ::FFI::Struct
-      layout \
-        :ctg,          :string,
-        :ctg_start,    :int32,
-        :ctg_end,      :int32,
-        :qry_start,    :int32,
-        :qry_end,      :int32,
-        :blen,         :int32,
-        :mlen,         :int32,
-        :NM,           :int32,
-        :ctg_len,      :int32,
-        :mapq,         :uint8_t,
-        :is_primary,   :uint8_t,
-        :strand,       :int8_t,
-        :trans_strand, :int8_t,
-        :seg_id,       :int32,
-        :n_cigar32,    :int32,
-        :cigar32,      :pointer
-    end
-
-    class KString < ::FFI::Struct
-      layout \
-        :l,            :size_t,
-        :m,            :size_t,
-        :s,            :string
-    end
-
-    class KSeq < ::FFI::Struct
-      layout \
-        :name,           KString,
-        :comment,        KString,
-        :seq,            KString,
-        :qual,           KString,
-        :last_char,      :int,
-        :f,              :pointer # KStream
-    end
-
-    attach_function \
-      :mm_reg2hitpy,
-      [Idx.by_ref, Reg1.by_ref, Hit.by_ref],
-      :void
-
-    attach_function \
-      :mm_free_reg1,
-      [Reg1.by_ref],
-      :void
-
-    attach_function \
-      :mm_fastx_open,
-      [:string],
-      KSeq.by_ref
-
-    attach_function \
-      :mm_fastx_close,
-      [KSeq.by_ref],
-      :void
-
-    attach_function \
-      :mm_verbose_level,
-      [:int],
-      :int
-
-    attach_function \
-      :mm_reset_timer,
-      [:void],
-      :void
-
-    attach_function \
-      :mm_map_aux,
-      [Idx.by_ref, :string, :string, :string, :pointer, TBuf.by_ref, MapOpt.by_ref],
-      :pointer # Reg1
-
-    attach_function \
-      :mappy_revcomp,
-      %i[int pointer],
-      :pointer
-
-    attach_function \
-      :mappy_free,
-      [:pointer],
-      :void
-
-    attach_function \
-      :mappy_fetch_seq,
-      [Idx.by_ref, :string, :int, :int, :pointer],
-      :pointer # Use pointer instead of string to read with a specified length
-
-    attach_function \
-      :mappy_idx_seq,
-      %i[int int int int string int],
-      Idx.by_ref
-
-    attach_function \
-      :kseq_read,
-      [KSeq.by_ref],
-      :int
-  end
-end

data/lib/minimap2/ffi.rb

@@ -1,27 +0,0 @@
-# frozen_string_literal: true
-
-# bit fields
-require "ffi/bit_struct"
-
-module Minimap2
-  # Native APIs
-  module FFI
-    extend ::FFI::Library
-    begin
-      ffi_lib Minimap2.ffi_lib
-    rescue LoadError => e
-      raise LoadError, "Could not find #{Minimap2.ffi_lib} \n#{e}"
-    end
-
-    # Continue even if some functions are not found.
-    def self.attach_function(*)
-      super
-    rescue ::FFI::NotFoundError => e
-      warn e.message
-    end
-  end
-end
-
-require_relative "ffi/constants"
-require_relative "ffi/functions"
-require_relative "ffi/mappy"