htslib 0.1.0 → 0.2.2

data/lib/hts/libhts.rb

@@ -4,6 +4,7 @@ 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
 

data/lib/hts/tbx.rb

@@ -8,7 +8,7 @@ module HTS
   class Tbx < Hts
     include Enumerable
 
-    attr_reader :file_name
+    attr_reader :file_name, :index_name, :mode, :nthreads
 
     def self.open(*args, **kw)
       file = new(*args, **kw) # do not yield
@@ -22,24 +22,55 @@ module HTS
       file
     end
 
-    def initialize(file_name, threads: nil)
+    def initialize(file_name, mode = "r", index: nil, threads: nil, build_index: false)
       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"
+      @file_name  = file_name
+      @index_name = index
+      @mode       = mode
+      @nthreads   = threads
       @hts_file = LibHTS.hts_open(@file_name, @mode)
 
       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
+      set_threads(threads) if threads
+
+      # return if @mode[0] == "w"
+      raise "Not implemented" if @mode[0] == "w"
+
+      # build_index(index) if build_index
+      @idx = load_index(index)
+
+      super # do nothing
+    end
+
+    def build_index
+      raise "Not implemented yet"
+    end
+
+    def load_index(index_name = nil)
+      if index_name
+        LibHTS.tbx_index_load2(@file_name, index_name)
+      else
+        LibHTS.tbx_index_load3(@file_name, nil, 2)
+      end
+    end
+
+    def tid(name)
+      LibHTS.tbx_name2id(@idx, name)
+    end
+
+    def seqnames
+      nseq = FFI::MemoryPointer.new(:int)
+      LibHTS.tbx_seqnames(@idx, nseq).then do |pts|
+        pts.read_array_of_pointer(nseq.read_int).map do |pt|
+          pt.read_string
+        end
       end
     end
   end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.1.0"
+  VERSION = "0.2.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.2
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-05-06 00:00:00.000000000 Z
+date: 2022-08-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -140,6 +140,7 @@ 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
@@ -158,6 +159,7 @@ files:
 - lib/hts/libhts/sam.rb
 - lib/hts/libhts/sam_funcs.rb
 - lib/hts/libhts/tbx.rb
+- lib/hts/libhts/tbx_funcs.rb
 - lib/hts/libhts/thread_pool.rb
 - lib/hts/libhts/vcf.rb
 - lib/hts/libhts/vcf_funcs.rb
@@ -176,7 +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:
   - - ">="