htslib 0.2.1 → 0.2.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 567d03329907f3f53424511f74a4c9fd6f745ef7c2b0c6c14e8dff6da957dbdb
+  metadata.gz: 93ee916dafed0ba04e486a59c81d2bd9befbceda3d679ef820e32d8817597afe
+  data.tar.gz: 7dda13879d0c3707354ab69fe9967f60f0300c1971011218a5cf79e5e211ee25
 SHA512:
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-  data.tar.gz: c62b5c7e95ba91a9f465b6822170c0faa05cf9626af8c63c486ecb55edb1af7f3d841cfa8b2d5adcd9cd1ac6df75088b85ea3145ae78a645eb2b7e3390ca11bd
+  metadata.gz: 8cf68e9276f353bdea4389f5584066870a4887f07891387cf143408cf215c43232f2c390c08b80c57225a8d8b3722a9dcc5ba5cc3cc716079cf004bd34df0da0
+  data.tar.gz: f30abf9c0d0dd07201e150dea5ec6976e7d968bc2f6bf2c347c1dec18cdfaaa5c141793208587f1629fa3cefeaaadd268083a105ab42dd450ce2ac8cfa0e2d7e

data/lib/hts/bam.rb

@@ -13,7 +13,7 @@ module HTS
   class Bam
     include Enumerable
 
-    attr_reader :file_name, :index_name, :mode, :header
+    attr_reader :file_name, :index_name, :mode, :header, :nthreads
 
     def self.open(*args, **kw)
       file = new(*args, **kw) # do not yield
@@ -28,7 +28,7 @@ module HTS
     end
 
     def initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil,
-                   create_index: false)
+                   build_index: false)
       if block_given?
         message = "HTS::Bam.new() dose not take block; Please use HTS::Bam.open() instead"
         raise message
@@ -39,6 +39,7 @@ module HTS
       @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?
@@ -53,21 +54,24 @@ module HTS
       return if @mode[0] == "w"
 
       @header = Bam::Header.new(@hts_file)
-      create_index(index) if create_index
+      build_index(index) if build_index
       @idx = load_index(index)
       @start_position = tell
       super # do nothing
     end
 
-    def create_index(index_name = nil)
+    def build_index(index_name = nil, min_shift: 0)
       check_closed
 
-      warn "Create index for #{@file_name} to #{index_name}"
-      if index
-        LibHTS.sam_index_build2(@file_name, index_name, -1)
+      if index_name
+        warn "Create index for #{@file_name} to #{index_name}"
       else
-        LibHTS.sam_index_build(@file_name, -1)
+        warn "Create index for #{@file_name}"
       end
+      r = LibHTS.sam_index_build3(@file_name, index_name, min_shift, @nthreads)
+      raise "Failed to build index for #{@file_name}" if r < 0
+
+      self
     end
 
     def load_index(index_name = nil)

data/lib/hts/bcf/record.rb

@@ -137,7 +137,7 @@ module HTS
 
       private
 
-      def initialize_copy(orig)\
+      def initialize_copy(orig)
         @header = orig.header
         @bcf1 = LibHTS.bcf_dup(orig.struct)
       end

data/lib/hts/bcf.rb

@@ -13,7 +13,7 @@ module HTS
   class Bcf < Hts
     include Enumerable
 
-    attr_reader :file_name, :index_name, :mode, :header
+    attr_reader :file_name, :index_name, :mode, :header, :nthreads
 
     def self.open(*args, **kw)
       file = new(*args, **kw) # do not yield
@@ -28,7 +28,7 @@ module HTS
     end
 
     def initialize(file_name, mode = "r", index: nil, threads: nil,
-                   create_index: false)
+                   build_index: false)
       if block_given?
         message = "HTS::Bcf.new() dose not take block; Please use HTS::Bcf.open() instead"
         raise message
@@ -39,6 +39,7 @@ module HTS
       @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?
@@ -48,21 +49,24 @@ module HTS
       return if @mode[0] == "w"
 
       @header = Bcf::Header.new(@hts_file)
-      create_index(index) if create_index
+      build_index(index) if build_index
       @idx = load_index(index)
       @start_position = tell
       super # do nothing
     end
 
-    def create_index(index_name = nil)
+    def build_index(index_name = nil, min_shift: 14)
       check_closed
 
-      warn "Create index for #{@file_name} to #{index_name}"
       if index_name
-        LibHTS.bcf_index_build2(@file_name, index_name, -1)
+        warn "Create index for #{@file_name} to #{index_name}"
       else
-        LibHTS.bcf_index_build(@file_name, -1)
+        warn "Create index for #{@file_name}"
       end
+      r = LibHTS.bcf_index_build3(@file_name, index_name, min_shift, @nthreads)
+      raise "Failed to build index for #{@file_name}" if r < 0
+
+      self
     end
 
     def load_index(index_name = nil)

data/lib/hts/hts.rb

@@ -69,13 +69,18 @@ module HTS
       @hts_file.nil? || @hts_file.null?
     end
 
-    def set_threads(n)
-      raise TypeError unless n.is_a(Integer)
-
-      if n > 0
-        r = LibHTS.hts_set_threads(@hts_file, n)
-        raise "Failed to set number of threads: #{threads}" if r < 0
+    def set_threads(n = nil)
+      if n.nil?
+        require "etc"
+        n = [Etc.nprocessors - 1, 1].max
       end
+      raise TypeError unless n.is_a?(Integer)
+      raise ArgumentError, "Number of threads must be positive" if n < 1
+
+      r = LibHTS.hts_set_threads(@hts_file, n)
+      raise "Failed to set number of threads: #{threads}" if r < 0
+
+      @nthreads = n
       self
     end
 

data/lib/hts/libhts/cram.rb

@@ -172,6 +172,31 @@ module HTS
       %i[cram_fd cram_fd int32],
       :int
 
+    attach_function \
+      :cram_slice_hdr_get_num_blocks,
+      [:pointer],
+      :int32
+
+    attach_function \
+      :cram_slice_hdr_get_embed_ref_id,
+      [:pointer],
+      :int
+
+    attach_function \
+      :cram_slice_hdr_get_coords,
+      %i[pointer pointer pointer pointer],
+      :void
+
+    attach_function \
+      :cram_decode_slice_header,
+      %i[pointer pointer],
+      :pointer
+
+    attach_function \
+      :cram_free_slice_header,
+      [:pointer],
+      :void
+
     attach_function \
       :cram_new_block,
       [CramContentType, :int],

data/lib/hts/libhts/sam.rb

@@ -685,6 +685,18 @@ module HTS
       :bam_mods_at_qpos,
       [Bam1, :int, :pointer, :pointer, :int],
       :int
+
+    # Returns data about a specific modification type for the alignment record.
+    attach_function \
+      :bam_mods_query_type,
+      %i[pointer int pointer pointer string],
+      :int
+
+    # Returns the list of base modification codes provided for this
+    attach_function \
+      :bam_mods_recorded,
+      %i[pointer pointer],
+      :int
   end
 end
 

data/lib/hts/libhts/sam_funcs.rb

@@ -34,11 +34,11 @@ module HTS
       end
 
       def bam_cigar_gen(l, o)
-        l << BAM_CIGAR_SHIFT | o
+        (l << BAM_CIGAR_SHIFT) | o
       end
 
       def bam_cigar_type(o)
-        BAM_CIGAR_TYPE >> (o << 1) & 3
+        (BAM_CIGAR_TYPE >> (o << 1)) & 3
       end
     end
 
@@ -91,7 +91,7 @@ module HTS
       end
 
       def bam_seqi(s, i)
-        s[i >> 1].read_uint8 >> ((~i & 1) << 2) & 0xf
+        (s[i >> 1].read_uint8 >> ((~i & 1) << 2)) & 0xf
       end
 
       def bam_set_seqi(s, i, b)

data/lib/hts/libhts/tbx.rb

@@ -59,7 +59,7 @@ module HTS
 
     attach_function \
       :tbx_seqnames,
-      [Tbx, :int],
+      [Tbx, :pointer],
       :pointer
 
     attach_function \

data/lib/hts/libhts/tbx_funcs.rb

@@ -0,0 +1,25 @@
+module HTS
+  module LibHTS
+    class << self
+      def tbx_itr_destroy(iter)
+        hts_itr_destroy(iter)
+      end
+
+      def tbx_itr_queryi(tbx, tid, beg, end_)
+        hts_itr_query(tbx[:idx], tid, beg, end_, tbx_readrec)
+      end
+
+      def tbx_itr_querys(tbx, s)
+        hts_itr_querys(tbx[:idx], s, @@tbx_name2id, tbx, @@hts_itr_query, @@tbx_readrec)
+      end
+
+      def tbx_itr_next(htsfp, tbx, itr, r)
+        hts_itr_next(hts_get_bgzfp(htsfp), itr, r, tbx)
+      end
+
+      def tbx_bgzf_itr_next(bgzfp, tbx, itr, r)
+        hts_itr_next(bgzfp, itr, r, tbx)
+      end
+    end
+  end
+end

data/lib/hts/libhts/vcf.rb

@@ -154,10 +154,12 @@ module HTS
       [BcfHdr, :int, KString],
       :int
 
-    attach_function \
-      :bcf_hdr_fmt_text,
-      [BcfHdr, :int, :pointer],
-      :string
+    # DEPRECATED
+    #
+    # attach_function \
+    #   :bcf_hdr_fmt_text,
+    #   [BcfHdr, :int, :pointer],
+    #   :string
 
     attach_function \
       :bcf_hdr_append,
@@ -274,6 +276,21 @@ module HTS
       [Bcf1, :int],
       :int
 
+    attach_function \
+      :bcf_has_variant_types,
+      [Bcf1, :uint32, :int],
+      :int
+
+    attach_function \
+      :bcf_has_variant_type,
+      [Bcf1, :int, :uint32],
+      :int
+
+    attach_function \
+      :bcf_variant_length,
+      [Bcf1, :int],
+      :int
+
     attach_function \
       :bcf_is_snp,
       [Bcf1],
@@ -433,6 +450,16 @@ module HTS
       :bcf_idx_save,
       [HtsFile],
       :int
+
+    attach_function \
+      :bcf_float_vector_end,
+      [],
+      :uint32
+
+    attach_function \
+      :bcf_float_missing,
+      [],
+      :uint32
   end
 end
 

data/lib/hts/libhts/vcf_funcs.rb

@@ -259,6 +259,25 @@ module HTS
       def bcf_index_seqnames(idx, hdr, nptr)
         hts_idx_seqnames(idx, nptr, @@bcf_hdr_id2name, hdr)
       end
+
+      # Typed value I/O
+      def bcf_int8_vector_end  = -127                       # INT8_MIN  + 1
+      def bcf_int16_vector_end = -32_767                    # INT16_MIN + 1
+      def bcf_int32_vector_end = -2_147_483_647             # INT32_MIN + 1
+      def bcf_int64_vector_end = -9_223_372_036_854_775_807 # INT64_MIN + 1
+      def bcf_str_vector_end   = 0
+      def bcf_int8_missing     = -128                             # INT8_MIN
+      def bcf_int16_missing    = (-32_767 - 1)                    # INT16_MIN
+      def bcf_int32_missing    = (-2_147_483_647 - 1)             # INT32_MIN
+      def bcf_int64_missing    = (-9_223_372_036_854_775_807 - 1) # INT64_MIN
+      def bcf_str_missing      = 0x07
+
+      BCF_MAX_BT_INT8  = 0x7f           # INT8_MAX  */
+      BCF_MAX_BT_INT16 = 0x7fff         # INT16_MAX */
+      BCF_MAX_BT_INT32 = 0x7fffffff     # INT32_MAX */
+      BCF_MIN_BT_INT8  = -120           # INT8_MIN  + 8 */
+      BCF_MIN_BT_INT16 = -32_760        # INT16_MIN + 8 */
+      BCF_MIN_BT_INT32 = -2_147_483_640 # INT32_MIN + 8 */
     end
   end
 end

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 +22,56 @@ 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?
 
       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
 end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.2.1"
+  VERSION = "0.2.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors:
 - kojix2
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-08-01 00:00:00.000000000 Z
+date: 2022-08-19 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: []
@@ -159,18 +159,18 @@ 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
 - 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
@@ -186,7 +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: []