htslib 0.0.10 → 0.2.1

data/lib/hts/libhts.rb

@@ -1,8 +1,10 @@
 # frozen_string_literal: true
 
 require_relative "ffi_ext/struct"
+require_relative "ffi_ext/pointer"
 
 module HTS
+  # A Module for working with native C HTSlib structures and functions.
   module LibHTS
     extend FFI::Library
 
@@ -12,6 +14,9 @@ module HTS
       raise LoadError, "#{e}\nCould not find #{HTS.lib_path}"
     end
 
+    # @!macro attach_function
+    #   @!method $1(${2--2})
+    #   @return [${-1}] the return value of $0
     def self.attach_function(*)
       super
     rescue FFI::NotFoundError => e

data/lib/hts/{tabix.rb → tbx.rb}

@@ -1,9 +1,11 @@
+# frozen_string_literal: true
+
 require_relative "../htslib"
 
 require_relative "hts"
 
 module HTS
-  class Tabix < Hts
+  class Tbx < Hts
     include Enumerable
 
     attr_reader :file_name
@@ -22,7 +24,7 @@ module HTS
 
     def initialize(file_name, threads: nil)
       if block_given?
-        message = "HTS::Tabix.new() dose not take block; Please use HTS::Tabix.open() instead"
+        message = "HTS::Tbx.new() dose not take block; Please use HTS::Tbx.open() instead"
         raise message
       end
 
@@ -35,19 +37,9 @@ module HTS
 
       raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
 
-      if threads&.> 0
-        r = LibHTS.hts_set_threads(@hts_file, threads)
-        raise "Failed to set number of threads: #{threads}" if r < 0
-      end
-    end
-
-    def close
-      LibHTS.hts_close(@hts_file)
-      @hts_file = nil
-    end
+      set_threads(threads) if threads
 
-    def closed?
-      @hts_file.nil?
+      super # do nothing
     end
   end
 end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.0.10"
+  VERSION = "0.2.1"
 end

data/lib/htslib.rb

@@ -40,6 +40,6 @@ module HTS
 
   autoload :Bam,    "hts/bam"
   autoload :Bcf,    "hts/bcf"
-  autoload :Tabix,  "hts/tabix"
+  autoload :Tbx,    "hts/tbx"
   autoload :Faidx,  "hts/faidx"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.10
+  version: 0.2.1
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-04-15 00:00:00.000000000 Z
+date: 2022-08-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -122,7 +122,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: 
+description:
 email:
 - 2xijok@gmail.com
 executables: []
@@ -132,6 +132,7 @@ files:
 - LICENSE.txt
 - README.md
 - lib/hts/bam.rb
+- lib/hts/bam/aux.rb
 - lib/hts/bam/cigar.rb
 - lib/hts/bam/flag.rb
 - lib/hts/bam/header.rb
@@ -139,10 +140,12 @@ files:
 - lib/hts/bcf.rb
 - lib/hts/bcf/format.rb
 - lib/hts/bcf/header.rb
+- lib/hts/bcf/header_record.rb
 - lib/hts/bcf/info.rb
 - lib/hts/bcf/record.rb
 - lib/hts/faidx.rb
 - lib/hts/ffi_ext/README.md
+- lib/hts/ffi_ext/pointer.rb
 - lib/hts/ffi_ext/struct.rb
 - lib/hts/hts.rb
 - lib/hts/libhts.rb
@@ -159,14 +162,15 @@ files:
 - lib/hts/libhts/thread_pool.rb
 - lib/hts/libhts/vcf.rb
 - lib/hts/libhts/vcf_funcs.rb
-- lib/hts/tabix.rb
+- lib/hts/tbx.rb
 - lib/hts/version.rb
 - lib/htslib.rb
+- vendor/libhts.dylib
 homepage: https://github.com/kojix2/ruby-htslib
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -174,7 +178,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.7'
+      version: '3.1'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
@@ -182,7 +186,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubygems_version: 3.3.7
-signing_key: 
+signing_key:
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []