htslib 0.2.6 → 0.2.9

data/lib/hts/libhts/constants.rb

@@ -570,5 +570,18 @@ module HTS
       :external,           4,
       :core,               5
     )
+
+    CramBlockMethod = enum(
+      :unknown,      -1,
+      :raw,          0,
+      :gzip,         1,
+      :bzip2,        2,
+      :lzma,         3,
+      :rans4x8,      4,
+      :ransnx16,     5,
+      :arith,        6,
+      :fqz,          7,
+      :tok3,         8
+    )
   end
 end

data/lib/hts/libhts/cram.rb

@@ -79,12 +79,27 @@ module HTS
       %i[cram_container int32 pointer],
       :void
 
+    attach_function \
+      :cram_container_get_num_records,
+      [:cram_container],
+      :int32
+
+    attach_function \
+      :cram_container_get_num_bases,
+      [:cram_container],
+      :int32
+
+    # Returns true if the container is empty (EOF marker)
     attach_function \
       :cram_container_is_empty,
       [:cram_fd],
       :int
 
-    # cram_block
+    # Returns chromosome and start/span from container struct
+    attach_function \
+      :cram_container_get_coords,
+      %i[cram_container pointer pointer],
+      :void
 
     attach_function \
       :cram_block_get_content_id,
@@ -116,6 +131,16 @@ module HTS
       [:cram_block],
       CramContentType
 
+    attach_function \
+      :cram_block_get_method,
+      [:cram_block],
+      CramBlockMethod
+
+    attach_function \
+      :cram_expand_method,
+      [:pointer, :int32, CramBlockMethod],
+      :pointer
+
     attach_function \
       :cram_block_set_content_id,
       %i[cram_block int32],
@@ -167,6 +192,18 @@ module HTS
       [:cram_block],
       :uint32
 
+    # Returns the Block Content ID values referred to by a cram_codec in ids[2].
+    attach_function \
+      :cram_codec_get_content_ids,
+      %i[pointer pointer],
+      :void
+
+    # Produces a human readable description of the codec parameters.
+    attach_function \
+      :cram_codec_describe,
+      [:pointer, KString.ptr],
+      :int
+
     # Renumbers RG numbers in a cram compression header.
     attach_function \
       :cram_transcode_rg,
@@ -180,6 +217,51 @@ module HTS
       %i[cram_fd cram_fd int32],
       :int
 
+    # Copies a container, but filtering it down to a specific region (as
+    # already specified in 'in'
+    attach_function \
+      :cram_filter_container,
+      %i[cram_fd cram_fd cram_container pointer],
+      :int
+
+    # Decodes a CRAM block compression header.
+    attach_function \
+      :cram_decode_compression_header,
+      %i[cram_fd cram_block],
+      :pointer # cram_block_compression_hdr
+
+    # Frees a cram_block_compression_hdr structure.
+    attach_function \
+      :cram_free_compression_header,
+      [:pointer],
+      :void
+
+    # Map cram block numbers to data-series.
+    attach_function \
+      :cram_update_cid2ds_map,
+      %i[pointer pointer],
+      :pointer
+
+    # Return a list of data series observed as belonging to a block with
+    # the specified content_id.
+    attach_function \
+      :cram_cid2ds_query,
+      %i[pointer int pointer],
+      :int
+
+    # Frees a cram_cid2ds_t allocated by cram_update_cid2ds_map
+    attach_function \
+      :cram_cid2ds_free,
+      [:pointer],
+      :void
+
+    # Produces a description of the record and tag encodings held within
+    # a compression header and appends to 'ks'.
+    attach_function \
+      :cram_describe_encodings,
+      [:pointer, KString.ptr],
+      :int
+
     # Returns the number of cram blocks within this slice.
     attach_function \
       :cram_slice_hdr_get_num_blocks,
@@ -360,5 +442,35 @@ module HTS
       :cram_get_refs,
       [HtsFile.by_ref],
       :pointer # refs_t
+
+    # Returns the file offsets of CRAM slices covering a specific region query.
+    attach_function \
+      :cram_index_extents,
+      %i[cram_fd int hts_pos_t hts_pos_t pointer pointer],
+      :int
+
+    # Returns the total number of containers in the CRAM index.
+    attach_function \
+      :cram_num_containers,
+      [:cram_fd],
+      :int64
+
+    # Returns the number of containers in the CRAM index within given offsets.
+    attach_function \
+      :cram_num_containers_between,
+      %i[cram_fd off_t off_t pointer pointer],
+      :int64
+
+    # Returns the byte offset for the start of the n^th container.
+    attach_function \
+      :cram_container_num2offset,
+      %i[cram_fd int64],
+      :off_t
+
+    # Returns the container number for the first container at offset >= pos.
+    attach_function \
+      :cram_container_offset2num,
+      %i[cram_fd off_t],
+      :int64
   end
 end

data/lib/hts/libhts/hts.rb

@@ -447,7 +447,7 @@ module HTS
     # Computes the final 128-bit MD5 hash from the given context
     attach_function \
       :hts_md5_final,
-      %i[pointer pointer], # unsinged char
+      %i[pointer pointer], # unsigned char
       :void
 
     #  Resets an md5_context to the initial state, as returned by hts_md5_init().

data/lib/hts/libhts/sam.rb

@@ -247,7 +247,7 @@ module HTS
        :hts_pos_t,
        :uint8,
        :size_t,
-       :string,
+       :pointer,
        :int32,
        :hts_pos_t,
        :hts_pos_t,
@@ -440,10 +440,22 @@ module HTS
       [SamHdr, Bam1, :pointer], # hts_filter_t
       :int
 
+    # Return a pointer to a BAM record's first aux field
+    attach_function \
+      :bam_aux_first,
+      [Bam1],
+      :pointer
+
+    # Return a pointer to a BAM record's next aux field
+    attach_function \
+      :bam_aux_next,
+      [Bam1, :pointer],
+      :pointer
+
     # Return a pointer to an aux record
     attach_function \
       :bam_aux_get,
-      [Bam1, :string], # FIXME
+      [Bam1, :string], # const char tag[2]
       :pointer
 
     # Get an integer aux value
@@ -500,6 +512,12 @@ module HTS
       [Bam1, :pointer],
       :int
 
+    # Delete an aux field from a BAM record. Identical to @c bam_aux_del() apart from the return value
+    attach_function \
+      :bam_aux_remove,
+      [Bam1, :pointer],
+      :pointer
+
     # Update or add a string-type tag
     attach_function \
       :bam_aux_update_str,
@@ -570,17 +588,17 @@ module HTS
       [:bam_plp],
       :void
 
-    callback :bam_plp_callback_funcion, [:pointer, Bam1, BamPileupCd], :int
+    callback :bam_plp_callback_function, [:pointer, Bam1, BamPileupCd], :int
 
     # sets a callback to initialise any per-pileup1_t fields.
     attach_function \
       :bam_plp_constructor,
-      %i[bam_plp bam_plp_callback_funcion],
+      %i[bam_plp bam_plp_callback_function],
       :void
 
     attach_function \
       :bam_plp_destructor,
-      %i[bam_plp bam_plp_callback_funcion],
+      %i[bam_plp bam_plp_callback_function],
       :void
 
     # Get pileup padded insertion sequence
@@ -632,12 +650,12 @@ module HTS
 
     attach_function \
       :bam_mplp_constructor,
-      %i[bam_mplp bam_plp_callback_funcion],
+      %i[bam_mplp bam_plp_callback_function],
       :void
 
     attach_function \
       :bam_mplp_destructor,
-      %i[bam_mplp bam_plp_callback_funcion],
+      %i[bam_mplp bam_plp_callback_function],
       :void
 
     attach_function \
@@ -662,12 +680,18 @@ module HTS
       [:pointer], # hts_base_mod_state
       :void
 
-    # Parses the Mm and Ml tags out of a bam record.
+    # Parses the MM and ML tags out of a bam record.
     attach_function \
       :bam_parse_basemod,
       [Bam1, :pointer],
       :int
 
+    # Parses the MM and ML tags out of a bam record.
+    attach_function \
+      :bam_parse_basemod2,
+      [Bam1, :pointer, :uint32],
+      :int
+
     # Returns modification status for the next base position in the query seq.
     attach_function \
       :bam_mods_at_next_pos,
@@ -692,6 +716,12 @@ module HTS
       %i[pointer int pointer pointer string],
       :int
 
+    # Returns data about the i^th modification type for the alignment record.
+    attach_function \
+      :bam_mods_queryi,
+      %i[pointer int pointer pointer string],
+      :int
+
     # Returns the list of base modification codes provided for this
     attach_function \
       :bam_mods_recorded,

data/lib/hts/libhts/tbx.rb

@@ -2,6 +2,13 @@
 
 module HTS
   module LibHTS
+    attach_variable :tbx_conf_gff, TbxConf
+    attach_variable :tbx_conf_bed, TbxConf
+    attach_variable :tbx_conf_psltbl, TbxConf
+    attach_variable :tbx_conf_sam, TbxConf
+    attach_variable :tbx_conf_vcf, TbxConf
+    attach_variable :tbx_conf_gaf, TbxConf
+
     attach_function \
       :tbx_name2id,
       [Tbx, :string],

data/lib/hts/libhts/tbx_funcs.rb

@@ -8,11 +8,16 @@ module HTS
       end
 
       def tbx_itr_queryi(tbx, tid, beg, end_)
-        hts_itr_query(tbx[:idx], tid, beg, end_, @@tbx_readrec)
+        hts_itr_query(tbx[:idx], tid, beg, end_, @ffi_functions[:tbx_readrec])
+      end
+
+      @@tbx_name2id = proc do |tbx, ss|
+        LibHTS.tbx_name2id(tbx, ss)
       end
 
       def tbx_itr_querys(tbx, s)
-        hts_itr_querys(tbx[:idx], s, @@tbx_name2id, tbx, @@hts_itr_query, @@tbx_readrec)
+        hts_itr_querys(tbx[:idx], s, @@tbx_name2id, tbx, @ffi_functions[:hts_itr_query],
+                       @ffi_functions[:tbx_readrec])
       end
 
       def tbx_itr_next(htsfp, tbx, itr, r)

data/lib/hts/libhts/vcf.rb

@@ -2,6 +2,12 @@
 
 module HTS
   module LibHTS
+    # Get error description for bcf error code
+    attach_function \
+      :bcf_strerror,
+      %i[int pointer size_t],
+      :string
+
     # Create an empty BCF header.
     attach_function \
       :bcf_hdr_init,

data/lib/hts/libhts/vcf_funcs.rb

@@ -272,7 +272,7 @@ module HTS
       alias bcf_itr_destroy hts_itr_destroy
 
       def bcf_itr_queryi(idx, tid, beg, _end)
-        hts_itr_query(idx, tid, beg, _end, @@bcf_readrec)
+        hts_itr_query(idx, tid, beg, _end, @ffi_functions[:bcf_readrec])
       end
 
       @@bcf_hdr_name2id = proc do |hdr, id|
@@ -280,7 +280,7 @@ module HTS
       end
 
       def bcf_itr_querys(idx, hdr, s)
-        hts_itr_querys(idx, s, @@bcf_hdr_name2id, hdr, @@hts_itr_query, @@bcf_readrec)
+        hts_itr_querys(idx, s, @@bcf_hdr_name2id, hdr, @ffi_functions[:hts_itr_query], @ffi_functions[:bcf_readrec])
       end
 
       # Load a BCF index

data/lib/hts/libhts.rb

@@ -37,5 +37,5 @@ require_relative "libhts/sam"
 require_relative "libhts/cram"
 require_relative "libhts/vcf"
 require_relative "libhts/tbx"
-require_relative "libhts/faidx"
+require_relative "libhts/fai"
 require_relative "libhts/thread_pool"

data/lib/hts/{tbx.rb → tabix.rb}

@@ -5,7 +5,7 @@ require_relative "../htslib"
 require_relative "hts"
 
 module HTS
-  class Tbx < Hts
+  class Tabix < Hts
     include Enumerable
 
     attr_reader :file_name, :index_name, :mode, :nthreads
@@ -22,9 +22,9 @@ module HTS
       file
     end
 
-    def initialize(file_name, mode = "r", index: nil, threads: nil, build_index: false)
+    def initialize(file_name, index: nil, threads: nil, build_index: false)
       if block_given?
-        message = "HTS::Tbx.new() dose not take block; Please use HTS::Tbx.open() instead"
+        message = "HTS::Tabix.new() dose not take block; Please use HTS::Tabix.open() instead"
         raise message
       end
 
@@ -32,17 +32,14 @@ module HTS
 
       @file_name  = file_name
       @index_name = index
-      @mode       = mode
+      @mode       = "r"
       @nthreads   = threads
-      @hts_file = LibHTS.hts_open(@file_name, @mode)
+      @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
 
-      # return if @mode[0] == "w"
-      raise "Not implemented" if @mode[0] == "w"
-
       # build_index(index) if build_index
       @idx = load_index(index)
     end
@@ -63,7 +60,7 @@ module HTS
       !@idx.null?
     end
 
-    def tid(name)
+    def name2id(name)
       LibHTS.tbx_name2id(@idx, name)
     end
 
@@ -79,7 +76,7 @@ module HTS
       raise "Index file is required to call the query method." unless index_loaded?
 
       if start && end_
-        queryi(tid(region), start, end_, &block)
+        queryi(name2id(region), start, end_, &block)
       else
         querys(region, &block)
       end
@@ -87,36 +84,33 @@ module HTS
 
     private
 
-    def queryi(id, start, end_)
+    def queryi(id, start, end_, &block)
       return to_enum(__method__, id, start, end_) unless block_given?
 
       qiter = LibHTS.tbx_itr_queryi(@idx, id, start, end_)
-
       raise "Failed to query region: #{id}:#{start}-#{end_}" if qiter.null?
 
-      r = LibHTS::KString.new
-      begin
-        yield r[:s] while LibHTS.tbx_itr_next(@hts_file, @idx, qiter, r) > 0
-      ensure
-        LibHTS.hts_itr_destroy(qiter)
-      end
+      query_yield(qiter, &block)
       self
     end
 
-    def querys(region)
+    def querys(region, &block)
       return to_enum(__method__, region) unless block_given?
 
       qiter = LibHTS.tbx_itr_querys(@idx, region)
-
       raise "Failed to query region: #{region}" if qiter.null?
 
+      query_yield(qiter, &block)
+      self
+    end
+
+    def query_yield(qiter)
       r = LibHTS::KString.new
       begin
         yield r[:s].split("\t") while LibHTS.tbx_itr_next(@hts_file, @idx, qiter, r) > 0
       ensure
         LibHTS.hts_itr_destroy(qiter)
       end
-      self
     end
   end
 end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.2.6"
+  VERSION = "0.2.9"
 end

data/lib/htslib.rb

@@ -55,6 +55,6 @@ module HTS
   autoload :Hts,    "hts/hts"
   autoload :Bam,    "hts/bam"
   autoload :Bcf,    "hts/bcf"
-  autoload :Tbx,    "hts/tbx"
   autoload :Faidx,  "hts/faidx"
+  autoload :Tabix,  "hts/tabix"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.6
+  version: 0.2.9
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-01-09 00:00:00.000000000 Z
+date: 2024-09-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -52,77 +52,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: irb
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: minitest
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: simplecov
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-description: 
+description:
 email:
 - 2xijok@gmail.com
 executables: []
@@ -155,7 +85,7 @@ files:
 - lib/hts/libhts/bgzf.rb
 - lib/hts/libhts/constants.rb
 - lib/hts/libhts/cram.rb
-- lib/hts/libhts/faidx.rb
+- lib/hts/libhts/fai.rb
 - lib/hts/libhts/hfile.rb
 - lib/hts/libhts/hts.rb
 - lib/hts/libhts/kfunc.rb
@@ -166,7 +96,7 @@ files:
 - lib/hts/libhts/thread_pool.rb
 - lib/hts/libhts/vcf.rb
 - lib/hts/libhts/vcf_funcs.rb
-- lib/hts/tbx.rb
+- lib/hts/tabix.rb
 - lib/hts/version.rb
 - lib/htslib.rb
 homepage: https://github.com/kojix2/ruby-htslib
@@ -174,7 +104,7 @@ licenses:
 - MIT
 metadata:
   msys2_mingw_dependencies: htslib
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -189,8 +119,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.1
-signing_key: 
+rubygems_version: 3.5.11
+signing_key:
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []