htslib 0.0.5 → 0.0.10

data/lib/hts/libhts/vcf_funcs.rb

@@ -0,0 +1,430 @@
+# frozen_string_literal: true
+
+module HTS
+  module LibHTS
+    attach_function \
+      :bcf_hdr_init,
+      [:string],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_destroy,
+      [BcfHdr],
+      :void
+
+    attach_function \
+      :bcf_init,
+      [],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_destroy,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_empty,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_clear,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_hdr_read,
+      [HtsFile],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_set_samples,
+      [BcfHdr, :string, :int],
+      :int
+
+    attach_function \
+      :bcf_subset_format,
+      [BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_hdr_write,
+      [HtsFile, BcfHdr],
+      :int
+
+    attach_function \
+      :vcf_parse,
+      [KString, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_open_mode,
+      %i[string string string],
+      :int
+
+    attach_function \
+      :vcf_format,
+      [BcfHdr, Bcf1, KString],
+      :int
+
+    attach_function \
+      :bcf_read,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_unpack,
+      [Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_dup,
+      [Bcf1],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_copy,
+      [Bcf1, Bcf1],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_write,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_hdr_read,
+      [HtsFile],
+      BcfHdr.by_ref
+
+    attach_function \
+      :vcf_hdr_write,
+      [HtsFile, BcfHdr],
+      :int
+
+    attach_function \
+      :vcf_read,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_write,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_readrec,
+      [BGZF, :pointer, :pointer, :pointer, :hts_pos_t, :hts_pos_t],
+      :int
+
+    attach_function \
+      :vcf_write_line,
+      [HtsFile, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_dup,
+      [BcfHdr],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_merge,
+      [BcfHdr, BcfHdr],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_add_sample,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_set,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_format,
+      [BcfHdr, :int, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_fmt_text,
+      [BcfHdr, :int, :pointer],
+      :string
+
+    attach_function \
+      :bcf_hdr_append,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_printf,
+      [BcfHdr, :string, :varargs],
+      :int
+
+    attach_function \
+      :bcf_hdr_get_version,
+      [BcfHdr],
+      :string
+
+    attach_function \
+      :bcf_hdr_set_version,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_remove,
+      [BcfHdr, :int, :string],
+      :void
+
+    attach_function \
+      :bcf_hdr_subset,
+      [BcfHdr, :int, :pointer, :pointer],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_seqnames,
+      [BcfHdr, :pointer],
+      :pointer
+
+    attach_function \
+      :bcf_hdr_parse,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_sync,
+      [BcfHdr],
+      :int
+
+    attach_function \
+      :bcf_hdr_parse_line,
+      [BcfHdr, :string, :pointer],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_format,
+      [BcfHrec, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_add_hrec,
+      [BcfHdr, BcfHrec],
+      :int
+
+    attach_function \
+      :bcf_hdr_get_hrec,
+      [BcfHdr, :int, :string, :string, :string],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_dup,
+      [BcfHrec],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_add_key,
+      [BcfHrec, :string, :size_t],
+      :int
+
+    attach_function \
+      :bcf_hrec_set_val,
+      [BcfHrec, :int, :string, :size_t, :int],
+      :int
+
+    attach_function \
+      :bcf_hrec_find_key,
+      [BcfHrec, :string],
+      :int
+
+    attach_function \
+      :hrec_add_idx,
+      [BcfHrec, :int],
+      :int
+
+    attach_function \
+      :bcf_hrec_destroy,
+      [BcfHrec],
+      :void
+
+    attach_function \
+      :bcf_subset,
+      [BcfHdr, Bcf1, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_translate,
+      [BcfHdr, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_get_variant_types,
+      [Bcf1],
+      :int
+
+    attach_function \
+      :bcf_get_variant_type,
+      [Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_is_snp,
+      [Bcf1],
+      :int
+
+    attach_function \
+      :bcf_update_filter,
+      [BcfHdr, Bcf1, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_add_filter,
+      [BcfHdr, Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_remove_filter,
+      [BcfHdr, Bcf1, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_has_filter,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_alleles,
+      [BcfHdr, Bcf1, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_update_alleles_str,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_id,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_add_id,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_info,
+      [BcfHdr, Bcf1, :string, :pointer, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_update_format_string,
+      [BcfHdr, Bcf1, :string, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_update_format,
+      [BcfHdr, Bcf1, :string, :pointer, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_get_fmt,
+      [BcfHdr, Bcf1, :string],
+      BcfFmt.by_ref
+
+    attach_function \
+      :bcf_get_info,
+      [BcfHdr, Bcf1, :string],
+      BcfInfo.by_ref
+
+    attach_function \
+      :bcf_get_fmt_id,
+      [Bcf1, :int],
+      BcfFmt.by_ref
+
+    attach_function \
+      :bcf_get_info_id,
+      [Bcf1, :int],
+      BcfInfo.by_ref
+
+    attach_function \
+      :bcf_get_info_values,
+      [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_get_format_string,
+      [BcfHdr, Bcf1, :string, :pointer, :pointer],
+      :int
+
+    attach_function \
+      :bcf_get_format_values,
+      [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_hdr_id2int,
+      [BcfHdr, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_fmt_array,
+      [KString, :int, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_fmt_sized_array,
+      [KString, :pointer],
+      :uint8_t
+
+    attach_function \
+      :bcf_enc_vchar,
+      [KString, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_enc_vint,
+      [KString, :int, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_enc_vfloat,
+      [KString, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_index_load2,
+      %i[string string],
+      HtsIdx.by_ref
+
+    attach_function \
+      :bcf_index_load3,
+      %i[string string int],
+      HtsIdx.by_ref
+
+    attach_function \
+      :bcf_index_build,
+      %i[string int],
+      :int
+
+    attach_function \
+      :bcf_index_build2,
+      %i[string string int],
+      :int
+
+    attach_function \
+      :bcf_index_build3,
+      %i[string string int int],
+      :int
+
+    attach_function \
+      :bcf_idx_init,
+      [HtsFile, BcfHdr, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_idx_save,
+      [HtsFile],
+      :int
+  end
+end

data/lib/hts/libhts.rb

@@ -23,11 +23,13 @@ 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/tabix.rb

@@ -1,28 +1,53 @@
-# frozen_string_literal: true
+require_relative "../htslib"
 
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
+require_relative "hts"
 
 module HTS
-  class Tabix
-    class << self
-      alias open new
+  class Tabix < 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
-      # IO like API
+
+    def initialize(file_name, threads: nil)
       if block_given?
-        begin
-          yield self
-        ensure
-          close
-        end
+        message = "HTS::Tabix.new() dose not take block; Please use HTS::Tabix.open() instead"
+        raise message
       end
-    end
 
-    def build; end
+      @file_name = file_name
+
+      # NOTE: Do not check for the existence of local files, since file_names may be remote URIs.
 
-    def sequences; end
+      @mode     = "r"
+      @hts_file = LibHTS.hts_open(@file_name, @mode)
 
-    # def __call__\
+      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
+
+    def closed?
+      @hts_file.nil?
+    end
   end
 end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.0.5"
+  VERSION = "0.0.10"
 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 :Tabix,  "hts/tabix"
+  autoload :Faidx,  "hts/faidx"
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.10
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-12-26 00:00:00.000000000 Z
+date: 2022-04-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -144,16 +144,21 @@ files:
 - lib/hts/faidx.rb
 - lib/hts/ffi_ext/README.md
 - 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
 - lib/hts/libhts/kfunc.rb
 - lib/hts/libhts/sam.rb
+- lib/hts/libhts/sam_funcs.rb
 - lib/hts/libhts/tbx.rb
+- lib/hts/libhts/thread_pool.rb
 - lib/hts/libhts/vcf.rb
+- lib/hts/libhts/vcf_funcs.rb
 - lib/hts/tabix.rb
 - lib/hts/version.rb
 - lib/htslib.rb
@@ -176,7 +181,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.3
+rubygems_version: 3.3.7
 signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby