Fix typo in docs

kojix2 · Mar 13, 2024 · 5cd57ed · 5cd57ed
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diff --git a/README.md b/README.md
@@ -23,7 +23,7 @@ gem install minimap2
     bundle install
     bundle exec rake minimap2:build
     bundle exec rake install
- 
+
 </details>
 
 ## Quick Start
@@ -36,6 +36,7 @@ seq     = aligner.seq("MT_human", 100, 200)
 hits    = aligner.align(seq)
 pp hits
 ```
+
 ```
 [#<Minimap2::Alignment:0x000055bbfde2d128
   @blen=100,
@@ -85,7 +86,7 @@ pp hits
       - trans_strand            Returns transcript strand. +1 if on the forward strand; -1 if on the reverse strand; 0 if unknown.
       - blen                    Returns length of the alignment, including both alignment matches and gaps but excluding ambiguous bases.
       - mlen                    Returns length of the matching bases in the alignment, excluding ambiguous base matches.
-      - nm                      Returns number of mismatches, gaps and ambiguous poistions in the alignment.
+      - nm                      Returns number of mismatches, gaps and ambiguous positions in the alignment.
       - primary                 Returns if the alignment is primary (typically the best and the first to generate).
       - q_st                    Returns start positions on the query.
       - q_en                    Returns end positions on the query.
@@ -104,19 +105,20 @@ pp hits
     * MapOpt class              Mapping options.
 ```
 
-* API is based on [Mappy](https://github.com/lh3/minimap2/tree/master/python), the official Python binding for Minimap2. 
-* `Aligner#map` has been changed to `align`, because `map` means iterator in Ruby.
-* See [documentation](https://kojix2.github.io/ruby-minimap2/) for details.
+- API is based on [Mappy](https://github.com/lh3/minimap2/tree/master/python), the official Python binding for Minimap2.
+- `Aligner#map` has been changed to `align`, because `map` means iterator in Ruby.
+- See [documentation](https://kojix2.github.io/ruby-minimap2/) for details.
 
 <details>
 <summary><b>C Structures and Functions</b></summary>
 
 ### FFI
-* Ruby-Minimap2 is built on top of [Ruby-FFI](https://github.com/ffi/ffi). 
-  * Native C functions can be called from the `Minimap2::FFI` module. 
-  * Native C structure members can be accessed.
-  * Bitfields are supported by [ffi-bitfield](https://github.com/kojix2/ffi-bitfield) gems.
-
+
+- Ruby-Minimap2 is built on top of [Ruby-FFI](https://github.com/ffi/ffi).
+  - Native C functions can be called from the `Minimap2::FFI` module.
+  - Native C structure members can be accessed.
+  - Bitfields are supported by [ffi-bitfield](https://github.com/kojix2/ffi-bitfield) gems.
+
 ```ruby
 aligner.idx_opt.members
 # => [:k, :w, :flag, :bucket_bits, :mini_batch_size, :batch_size]
@@ -128,15 +130,15 @@ aligner.idx_opt[:k] = 14
 aligner.idx_opt[:k]
 # => 14
 ```
- 
+
 </details>
 
 ## Contributing
 
 <details>
 <summary><b>Development</b></summary>
 
- Fork your repository.
+Fork your repository.
 then clone.
 
 ```sh
@@ -182,7 +184,7 @@ ruby-minimap2 is a library under development and there are many points to be imp
 
 Please feel free to report [bugs](https://github.com/kojix2/ruby-minimap2/issues) and [pull requests](https://github.com/kojix2/ruby-minimap2/pulls)!
 
-Many OSS projects become abandoned because only the founder has commit rights to the original repository. 
+Many OSS projects become abandoned because only the founder has commit rights to the original repository.
 If you need commit rights to ruby-minimap2 repository or want to get admin rights and take over the project, please feel free to contact me @kojix2.
 
 ## License

diff --git a/lib/minimap2.rb b/lib/minimap2.rb
@@ -76,7 +76,7 @@ def verbose=(level)
     # @param [String] file_path
     # @param [Boolean] comment If True, the comment will be read.
     # @yield [name, seq, qual, comment]
-    # @return [Enumerator] enum Retrun Enumerator if not block given.
+    # @return [Enumerator] enum Return Enumerator if not block given.
     # Note: You can BioRuby instead of this method.
 
     def fastx_read(file_path, comment: false, &block)

diff --git a/lib/minimap2/aligner.rb b/lib/minimap2/aligner.rb
@@ -21,10 +21,11 @@ class Aligner
     #   * ava-ont : Nanopore read overlap
     # @param k [Integer] k-mer length, no larger than 28.
     # @param w [Integer] minimizer window size, no larger than 255.
-    # @param min_cnt [Integer] mininum number of minimizers on a chain.
-    # @param min_chain_score [Integer] minimum chaing score.
+    # @param min_cnt [Integer] minimum number of minimizers on a chain.
+    # @param min_chain_score [Integer] minimum chain score.
     # @param min_dp_score
-    # @param bw [Integer] chaining and alignment band width.
+    # @param bw [Integer] chaining and alignment band width. (initial chaining and extension)
+    # @param bw_long [Integer] chaining and alignment band width (RMQ-based rechaining and closing gaps)
     # @param best_n [Integer] max number of alignments to return.
     # @param n_threads [Integer] number of indexing threads.
     # @param fn_idx_out [String] name of file to which the index is written.

diff --git a/lib/minimap2/alignment.rb b/lib/minimap2/alignment.rb
@@ -23,7 +23,7 @@ module Minimap2
   #   @return [Integer] length of the matching bases in the alignment,
   #     excluding ambiguous base matches.
   # @!attribute nm
-  #   @return [Integer] number of mismatches, gaps and ambiguous poistions in the alignment.
+  #   @return [Integer] number of mismatches, gaps and ambiguous positions in the alignment.
   # @!attribute primary
   #   @return [Integer] if the alignment is primary (typically the best and the first to generate)
   # @!attribute q_st