minimap2 0.0.2 → 0.0.3

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

@@ -4,6 +4,9 @@
 [![CI](https://github.com/kojix2/ruby-minimap2/workflows/CI/badge.svg)](https://github.com/kojix2/ruby-minimap2/actions)
 [![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
 [![Docs Latest](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/minimap2)
+[![DOI](https://zenodo.org/badge/325711305.svg)](https://zenodo.org/badge/latestdoi/325711305)
+
+
 
 :dna: [minimap2](https://github.com/lh3/minimap2) - the long-read mapper - for [Ruby](https://github.com/ruby/ruby)
 
@@ -14,7 +17,7 @@ You need to install ruby-minimap2 from the source code. Because you need to buil
 Build
 
 ```sh
-git clone --recurse-submodules https://github.com/kojix2/ruby-minimap2
+git clone --recursive https://github.com/kojix2/ruby-minimap2
 cd ruby-minimap2
 bundle install
 bundle exec rake minimap2:build
@@ -40,27 +43,26 @@ aligner = Minimap2::Aligner.new("minimap2/test/MT-human.fa")
 seq = aligner.seq("MT_human", 100, 200)
 
 # mapping
-aligner.align(seq) do |h|
-  pp h.to_h
-  # {:ctg          => "MT_human",
-  #  :ctg_len      => 16569,
-  #  :r_st         => 100,
-  #  :r_en         => 200,
-  #  :strand       => 1,
-  #  :trans_strand => 0,
-  #  :blen         => 100,
-  #  :mlen         => 100,
-  #  :nm           => 0,
-  #  :primary      => 1,
-  #  :q_st         => 0,
-  #  :q_en         => 100,
-  #  :mapq         => 60,
-  #  :cigar        => [[100, 0]],
-  #  :read_num     => 1,
-  #  :cs           => "",
-  #  :md           => "",
-  #  :cigar_str    => "100M"}
-end
+hits = aligner.align(seq)
+pp hits[0].to_h
+# {:ctg          => "MT_human",
+#  :ctg_len      => 16569,
+#  :r_st         => 100,
+#  :r_en         => 200,
+#  :strand       => 1,
+#  :trans_strand => 0,
+#  :blen         => 100,
+#  :mlen         => 100,
+#  :nm           => 0,
+#  :primary      => 1,
+#  :q_st         => 0,
+#  :q_en         => 100,
+#  :mapq         => 60,
+#  :cigar        => [[100, 0]],
+#  :read_num     => 1,
+#  :cs           => "",
+#  :md           => "",
+#  :cigar_str    => "100M"}
 ```
 
 ## APIs Overview
@@ -121,7 +123,7 @@ ruby-minimap2 is built on top of [Ruby-FFI](https://github.com/ffi/ffi). Native
 Fork your repository and clone.
 
 ```sh
-git clone --recurse-submodules https://github.com/kojix2/ruby-minimap2
+git clone --recursive https://github.com/kojix2/ruby-minimap2
 # git clone https://github.com/kojix2/ruby-minimap2
 # cd ruby-minimap2
 # git submodule update -i

data/lib/minimap2/aligner.rb

@@ -80,7 +80,7 @@ module Minimap2
       end
 
       if fn_idx_in
-        warn "Since fn_idx_in is specified, the seq argument will be ignored." if seq
+        warn 'Since fn_idx_in is specified, the seq argument will be ignored.' if seq
         reader = FFI.mm_idx_reader_open(fn_idx_in, idx_opt, fn_idx_out)
 
         # The Ruby version raises an error here
@@ -116,6 +116,7 @@ module Minimap2
     #   In the Ruby language, the name map means iterator.
     #   The original name is map, but here I use the method name align.
     # @note The use of Enumerator is being considered. The method names may change again.
+    # @return [Array] alignments
 
     def align(
       seq, seq2 = nil,
@@ -133,25 +134,29 @@ module Minimap2
 
       buf ||= FFI::TBuf.new
       km = FFI.mm_tbuf_get_km(buf)
-      n_regs_ptr = ::FFI::MemoryPointer.new :int
 
-      ptr = FFI.mm_map_aux(index, seq, seq2, n_regs_ptr, buf, map_opt)
+      n_regs_ptr = ::FFI::MemoryPointer.new :int
+      regs_ptr = FFI.mm_map_aux(index, seq, seq2, n_regs_ptr, buf, map_opt)
       n_regs = n_regs_ptr.read_int
 
-      regs = Array.new(n_regs) { |i| FFI::Reg1.new(ptr + i * FFI::Reg1.size) }
+      regs = Array.new(n_regs) do |i|
+        FFI::Reg1.new(regs_ptr + i * FFI::Reg1.size)
+      end
 
       hit = FFI::Hit.new
+
       cs_str     = ::FFI::MemoryPointer.new(::FFI::MemoryPointer.new(:string))
       m_cs_str   = ::FFI::MemoryPointer.new :int
+
+      alignments = []
+
       i = 0
       begin
         while i < n_regs
           FFI.mm_reg2hitpy(index, regs[i], hit)
-          cigar = []
 
           c = hit[:cigar32].read_array_of_uint32(hit[:n_cigar32])
-          # convert the 32-bit CIGAR encoding to Ruby array
-          cigar = c.map { |x| [x >> 4, x & 0xf] }
+          cigar = c.map { |x| [x >> 4, x & 0xf] } # 32-bit CIGAR encoding -> Ruby array
 
           _cs = ''
           if cs
@@ -165,7 +170,7 @@ module Minimap2
             _md = cs_str.read_pointer.read_string(l_cs_str)
           end
 
-          yield Alignment.new(hit, cigar, _cs, _md)
+          alignments << Alignment.new(hit, cigar, _cs, _md)
 
           FFI.mm_free_reg1(regs[i])
           i += 1
@@ -176,6 +181,7 @@ module Minimap2
           i += 1
         end
       end
+      alignments
     end
 
     # retrieve a subsequence from the index.
@@ -193,11 +199,13 @@ module Minimap2
     end
 
     # k-mer length, no larger than 28
+
     def k
       index[:k]
     end
 
     # minimizer window size, no larger than 255
+
     def w
       index[:w]
     end

data/lib/minimap2/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Minimap2
-  VERSION = '0.0.2'
+  VERSION = '0.0.3'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-14 00:00:00.000000000 Z
+date: 2021-04-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi