htslib 0.0.8 → 0.2.0

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
@@ -23,12 +28,13 @@ end
 require_relative "libhts/constants"
 
 # This is alphabetical order.
+require_relative "libhts/kfunc"
 require_relative "libhts/bgzf"
-require_relative "libhts/faidx"
 require_relative "libhts/hfile"
 require_relative "libhts/hts"
 require_relative "libhts/sam"
-require_relative "libhts/kfunc"
-require_relative "libhts/tbx"
+require_relative "libhts/cram"
 require_relative "libhts/vcf"
+require_relative "libhts/tbx"
+require_relative "libhts/faidx"
 require_relative "libhts/thread_pool"

data/lib/hts/tbx.rb

@@ -0,0 +1,45 @@
+# frozen_string_literal: true
+
+require_relative "../htslib"
+
+require_relative "hts"
+
+module HTS
+  class Tbx < Hts
+    include Enumerable
+
+    attr_reader :file_name
+
+    def self.open(*args, **kw)
+      file = new(*args, **kw) # do not yield
+      return file unless block_given?
+
+      begin
+        yield file
+      ensure
+        file.close
+      end
+      file
+    end
+
+    def initialize(file_name, threads: nil)
+      if block_given?
+        message = "HTS::Tbx.new() dose not take block; Please use HTS::Tbx.open() instead"
+        raise message
+      end
+
+      @file_name = file_name
+
+      # NOTE: Do not check for the existence of local files, since file_names may be remote URIs.
+
+      @mode     = "r"
+      @hts_file = LibHTS.hts_open(@file_name, @mode)
+
+      raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
+
+      set_threads(threads) if threads
+
+      super # do nothing
+    end
+  end
+end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.0.8"
+  VERSION = "0.2.0"
 end

data/lib/htslib.rb

@@ -37,9 +37,9 @@ module HTS
   # You can change the path of the shared library with `HTS.lib_path=`
   # before calling the LibHTS module.
   autoload :LibHTS, "hts/libhts"
-end
 
-require_relative "hts/bam"
-require_relative "hts/faidx"
-require_relative "hts/tabix"
-require_relative "hts/bcf"
+  autoload :Bam,    "hts/bam"
+  autoload :Bcf,    "hts/bcf"
+  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: 0.0.8
+  version: 0.2.0
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-03-15 00:00:00.000000000 Z
+date: 2022-05-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -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
@@ -143,10 +144,13 @@ files:
 - 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
 - lib/hts/libhts/bgzf.rb
 - lib/hts/libhts/constants.rb
+- lib/hts/libhts/cram.rb
 - lib/hts/libhts/faidx.rb
 - lib/hts/libhts/hfile.rb
 - lib/hts/libhts/hts.rb
@@ -157,7 +161,7 @@ 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
 homepage: https://github.com/kojix2/ruby-htslib
@@ -172,7 +176,7 @@ 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:
   - - ">="

data/lib/hts/tabix.rb

@@ -1,28 +0,0 @@
-# frozen_string_literal: true
-
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
-module HTS
-  class Tabix
-    class << self
-      alias open new
-    end
-    def initialize
-      # IO like API
-      if block_given?
-        begin
-          yield self
-        ensure
-          close
-        end
-      end
-    end
-
-    def build; end
-
-    def sequences; end
-
-    # def __call__\
-  end
-end