ruby-minigraph 0.0.20.0 → 0.0.20.1

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@@ -1,7 +1,7 @@
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data/README.md

@@ -12,7 +12,12 @@
 
 ## Installation
 
-You need to install it from the source code. Because you need to build minigraph and create a shared library. Open your terminal and type the following commands in order. 
+```sh
+gem install ruby-minigraph
+```
+
+<details>
+<summary><b>Compiling from source</b></summary>
 
 ```sh
 git clone --recursive https://github.com/kojix2/ruby-minigraph
@@ -22,20 +27,47 @@ bundle exec rake minigraph:build
 bundle exec rake install
 ```
 
-You can run tests to see if the installation was successful. 
-
-```
-bundle exec rake test
-```
+</details>
 
 ## Quick Start
 
 ```ruby
 require "minigraph"
+
+Minigraph.execute("--version")
 ```
 
 ## APIs
 
+Only low-level functions are provided at this time.
+
+```ruby
+require "minigraph"
+
+MG = Minigraph
+
+n_threads = 4
+
+target = "ext/minigraph/test/MT-human.fa"
+queries = ["ext/minigraph/test/MT-orangeA.fa"]
+
+opt = MG::FFI::MapOpt.new
+ipt = MG::FFI::IdxOpt.new
+gpt = MG::FFI::GGOpt.new
+
+MG::FFI.mg_opt_set(0, ipt, opt, gpt)
+
+g = MG::FFI.gfa_read(target)
+
+ptr = FFI::MemoryPointer.new(:pointer, queries.length)
+ptrs = queries.map{ FFI::MemoryPointer.from_string(_1) }
+ptr.write_array_of_pointer(ptrs)
+
+MG::FFI.mg_map_files(g, 1, ptr, ipt, opt, n_threads)
+
+MG::FFI.gfa_destroy(g)
+```
+
 ## Development
 
 ```sh

data/lib/minigraph/ffi/constants.rb

@@ -66,8 +66,8 @@ module Minigraph
     # indexing option
     class IdxOpt < ::FFI::Struct
       layout \
-        :k,               :int,
         :w,               :int,
+        :k,               :int,
         :bucket_bits,     :int
     end
 

data/lib/minigraph/ffi/functions.rb

@@ -9,10 +9,22 @@ module Minigraph
 
     # options
     attach_function \
-      :mg_opt_set,
-      [:string, IdxOpt.by_ref, MapOpt.by_ref, GGOpt.by_ref],
+      :mg_opt_set_raw, :mg_opt_set,
+      [:pointer, IdxOpt.by_ref, MapOpt.by_ref, GGOpt.by_ref],
       :int
 
+    private_class_method :mg_opt_set_raw
+
+    def self.mg_opt_set(preset, io, mo, go)
+      ptr = case preset
+            when 0, nil
+              ::FFI::Pointer.new(:int, 0)
+            else
+              ::FFI::MemoryPointer.from_string(preset.to_s)
+            end
+      mg_opt_set_raw(ptr, io, mo, go)
+    end
+
     attach_function \
       :mg_opt_check,
       [IdxOpt.by_ref, MapOpt.by_ref, GGOpt.by_ref],
@@ -66,5 +78,47 @@ module Minigraph
       :mg_ggen,
       [:pointer, :int32, :pointer, IdxOpt.by_ref, MapOpt.by_ref, GGOpt.by_ref, :int], # FIXME: gfa_t
       :int
+
+    attach_function \
+      :mg_idxopt_init,
+      [IdxOpt.by_ref],
+      :void
+
+    attach_function \
+      :mg_mapopt_init,
+      [MapOpt.by_ref],
+      :void
+
+    attach_function \
+      :mg_ggopt_init,
+      [GGOpt.by_ref],
+      :void
+
+    # gfa.h
+
+    attach_function \
+      :gfa_init,
+      [:void],
+      :pointer # gfa_t *
+
+    attach_function \
+      :gfa_destroy,
+      [:pointer], # gfa_t *
+      :void
+
+    attach_function \
+      :gfa_read,
+      [:string],
+      :pointer # gfa_t *
+
+    attach_function \
+      :gfa_print,
+      %i[pointer pointer int],
+      :void
+
+    attach_function \
+      :gfa_sort_ref_arc,
+      [:pointer], # gfa_t *
+      :void
   end
 end

data/lib/minigraph/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Minigraph
-  VERSION = "0.0.20.0"
+  VERSION = "0.0.20.1"
 end

data/lib/minigraph.rb

@@ -10,6 +10,7 @@ require_relative "minigraph/version"
 # https://github.com/lh3/minigraph
 # Li, H., Feng, X. & Chu, C. The design and construction of reference pangenome graphs
 # with minigraph. Genome Biol 21, 265 (2020). https://doi.org/10.1186
+
 module Minigraph
   class Error < StandardError; end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ruby-minigraph
 version: !ruby/object:Gem::Version
-  version: 0.0.20.0
+  version: 0.0.20.1
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-05-21 00:00:00.000000000 Z
+date: 2023-06-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -137,7 +137,7 @@ homepage: https://github.com/kojix2/ruby-minigraph
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -153,7 +153,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubygems_version: 3.4.10
-signing_key: 
+signing_key:
 specification_version: 4
 summary: Ruby bindings for minigraph
 test_files: []