minimap2 0.2.24.1 → 0.2.24.3

checksums.yaml

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

@@ -2,8 +2,9 @@
 
 [![Gem Version](https://img.shields.io/gem/v/minimap2?color=brightgreen)](https://rubygems.org/gems/minimap2)
 [![CI](https://github.com/kojix2/ruby-minimap2/workflows/CI/badge.svg)](https://github.com/kojix2/ruby-minimap2/actions)
+[![Docs Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/minimap2)
+[![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://kojix2.github.io/ruby-minimap2/)
 [![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)
@@ -107,7 +108,7 @@ pp hits
 
 * 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 [RubyDoc](https://rubydoc.info/gems/minimap2/) for details.
+* See [documentation](https://kojix2.github.io/ruby-minimap2/) for details.
 
 <details>
 <summary><b>C Structures and Functions</b></summary>
@@ -174,6 +175,10 @@ 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)!
 
+    Do you need commit rights to my repository?
+    Do you want to get admin rights and take over the project?
+    If so, please feel free to contact me @kojix2.
+
 ## License
 
 [MIT License](https://opensource.org/licenses/MIT).

data/lib/minimap2/aligner.rb

@@ -140,8 +140,8 @@ module Minimap2
 
       return if index.null?
 
-      map_opt.max_frag_len = max_frag_len if max_frag_len
-      map_opt.flag |= extra_flags if extra_flags
+      map_opt[:max_frag_len] = max_frag_len if max_frag_len
+      map_opt[:flag] |= extra_flags if extra_flags
 
       buf ||= FFI::TBuf.new
       km = FFI.mm_tbuf_get_km(buf)

data/lib/minimap2/ffi/constants.rb

@@ -135,9 +135,9 @@ module Minimap2
         :pe_bonus,             :int,
         :mid_occ_frac,         :float,   # only used by mm_mapopt_update(); see below
         :q_occ_frac,           :float,
-        :min_mid_occ,          :int32_t,
-        :mid_occ,              :int32_t, # ignore seeds with occurrences above this threshold
-        :max_occ,              :int32_t,
+        :min_mid_occ,          :int32,
+        :mid_occ,              :int32, # ignore seeds with occurrences above this threshold
+        :max_occ,              :int32,
         :mini_batch_size,      :int64_t, # size of a batch of query bases to process in parallel
         :max_sw_mat,           :int64_t,
         :cap_kalloc,           :int64_t,
@@ -149,19 +149,19 @@ module Minimap2
       layout \
         :name,   :string,    # name of the db sequence
         :offset, :uint64_t,  # offset in mm_idx_t::S
-        :len,    :uint32_t,  # length
-        :is_alt, :uint32_t
+        :len,    :uint32,  # length
+        :is_alt, :uint32
     end
 
     class Idx < ::FFI::Struct
       layout \
-        :b,     :int32_t,
-        :w,     :int32_t,
-        :k,     :int32_t,
-        :flag,  :int32_t,
-        :n_seq, :uint32_t,   # number of reference sequences
-        :index, :int32_t,
-        :n_alt, :int32_t,
+        :b,     :int32,
+        :w,     :int32,
+        :k,     :int32,
+        :flag,  :int32,
+        :n_seq, :uint32,   # number of reference sequences
+        :index, :int32,
+        :n_alt, :int32,
         :seq,   IdxSeq.ptr,  # sequence name, length and offset
         :S,     :pointer,    # 4-bit packed sequence
         :B,     :pointer,    # index (hidden)
@@ -203,23 +203,23 @@ module Minimap2
 
     class Reg1 < ::FFI::BitStruct
       layout \
-        :id,     :int32_t, # ID for internal uses (see also parent below)
-        :cnt,    :int32_t, # number of minimizers; if on the reverse strand
-        :rid,    :int32_t, # reference index; if this is an alignment from inversion rescue
-        :score,  :int32_t, # DP alignment score
-        :qs,     :int32_t, # query start
-        :qe,     :int32_t, # query end
-        :rs,     :int32_t, # reference start
-        :re,     :int32_t, # reference end
-        :parent, :int32_t, # parent==id if primary
-        :subsc,  :int32_t, # best alternate mapping score
-        :as,     :int32_t, # offset in the a[] array (for internal uses only)
-        :mlen,   :int32_t, # seeded exact match length
-        :blen,   :int32_t, # seeded alignment block length
-        :n_sub,  :int32_t, # number of suboptimal mappings
-        :score0, :int32_t, # initial chaining score (before chain merging/spliting)
-        :fields, :uint32_t,
-        :hash,   :uint32_t,
+        :id,     :int32, # ID for internal uses (see also parent below)
+        :cnt,    :int32, # number of minimizers; if on the reverse strand
+        :rid,    :int32, # reference index; if this is an alignment from inversion rescue
+        :score,  :int32, # DP alignment score
+        :qs,     :int32, # query start
+        :qe,     :int32, # query end
+        :rs,     :int32, # reference start
+        :re,     :int32, # reference end
+        :parent, :int32, # parent==id if primary
+        :subsc,  :int32, # best alternate mapping score
+        :as,     :int32, # offset in the a[] array (for internal uses only)
+        :mlen,   :int32, # seeded exact match length
+        :blen,   :int32, # seeded alignment block length
+        :n_sub,  :int32, # number of suboptimal mappings
+        :score0, :int32, # initial chaining score (before chain merging/spliting)
+        :fields, :uint32,
+        :hash,   :uint32,
         :div,    :float,
         :p,      Extra.ptr
 

data/lib/minimap2/ffi/mappy.rb

@@ -7,20 +7,20 @@ module Minimap2
     class Hit < ::FFI::Struct
       layout \
         :ctg,          :string,
-        :ctg_start,    :int32_t,
-        :ctg_end,      :int32_t,
-        :qry_start,    :int32_t,
-        :qry_end,      :int32_t,
-        :blen,         :int32_t,
-        :mlen,         :int32_t,
-        :NM,           :int32_t,
-        :ctg_len,      :int32_t,
+        :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_t,
-        :n_cigar32,    :int32_t,
+        :seg_id,       :int32,
+        :n_cigar32,    :int32,
         :cigar32,      :pointer
     end
 

data/lib/minimap2/version.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
 module Minimap2
-  # Minimap2-2.23 (r1111)
-  VERSION = "0.2.24.1"
+  #  Minimap2-2.24 (r1122)
+  VERSION = "0.2.24.3"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.24.1
+  version: 0.2.24.3
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-12-29 00:00:00.000000000 Z
+date: 2023-04-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -164,7 +164,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.3
+rubygems_version: 3.4.10
 signing_key: 
 specification_version: 4
 summary: minimap2