htslib 0.2.3 → 0.2.6

data/lib/hts/hts.rb

@@ -31,8 +31,8 @@ module HTS
       end
     end
 
-    def initialize(*args)
-      # do nothing
+    def initialize(*_args)
+      raise TypeError, "Can't make instance of HTS abstract class"
     end
 
     def struct
@@ -69,6 +69,11 @@ module HTS
       @hts_file.nil? || @hts_file.null?
     end
 
+    def fai=(fai)
+      check_closed
+      LibHTS.hts_set_fai_filename(@hts_file, fai) > 0 || raise
+    end
+
     def set_threads(n = nil)
       if n.nil?
         require "etc"
@@ -107,14 +112,12 @@ module HTS
     end
 
     def rewind
-      if @start_position
-        r = seek(@start_position)
-        raise "Failed to rewind: #{r}" if r < 0
+      raise "Cannot rewind: no start position" unless @start_position
 
-        tell
-      else
-        raise "Cannot rewind: no start position"
-      end
+      r = seek(@start_position)
+      raise "Failed to rewind: #{r}" if r < 0
+
+      tell
     end
 
     private

data/lib/hts/libhts/constants.rb

@@ -158,7 +158,7 @@ module HTS
         :specific,          :pointer
     end
 
-    class HtsIdx < FFI::Struct
+    class HtsIdx < FFI::Struct # FIXME: ManagedStruct
       layout \
         :fmt,            :int,
         :min_shift,      :int,
@@ -188,6 +188,10 @@ module HTS
           :n_mapped,     :uint64,
           :n_unmapped,   :uint64
         )
+
+      def self.release(ptr)
+        LibHTS.hts_idx_destroy(ptr) unless ptr.null?
+      end
     end
 
     class HtsReglist < FFI::Struct
@@ -201,7 +205,7 @@ module HTS
     end
 
     # HtsFile
-    class SamHdr < FFI::Struct
+    class SamHdr < FFI::ManagedStruct
       layout \
         :n_targets,      :int32,
         :ignore_sam_err, :int32,
@@ -213,6 +217,10 @@ module HTS
         :sdict,          :pointer,
         :hrecs,          :pointer,
         :ref_count,      :uint32
+
+      def self.release(ptr)
+        LibHTS.sam_hdr_destroy(ptr) unless ptr.null?
+      end
     end
 
     BamHdr = SamHdr
@@ -247,10 +255,14 @@ module HTS
 
     SamFile = HtsFile
 
-    class HtsTpool < FFI::Struct
+    class HtsTpool < FFI::ManagedStruct
       layout \
         :pool,           :pointer,
         :qsize,          :int
+
+      def self.release(ptr)
+        LibHTS.hts_tpool_destroy(ptr) unless ptr.null?
+      end
     end
 
     class HtsOpt < FFI::Struct
@@ -265,7 +277,7 @@ module HTS
         :next,           HtsOpt.ptr
     end
 
-    class HtsItr < FFI::BitStruct
+    class HtsItr < FFI::BitStruct # FIXME: ManagedBitStruct
       layout \
         :_flags,         :uint32, # bit_fields
         :tid,            :int,
@@ -300,6 +312,10 @@ module HTS
                  :nocoor,    1,
                  :multi,     1,
                  :dummy,     27
+
+      def self.release(ptr)
+        LibHTS.hts_itr_destroy(ptr) unless ptr.null?
+      end
     end
 
     class Bam1Core < FFI::Struct
@@ -342,14 +358,14 @@ module HTS
     class BamPileupCd < FFI::Union
       layout \
         :p,               :pointer,
-        :i,               :int64_t,
+        :i,               :int64,
         :f,               :double
     end
 
     class BamPileup1 < FFI::BitStruct
       layout \
         :b,              Bam1.ptr,
-        :qpos,           :int32_t,
+        :qpos,           :int32,
         :indel,          :int,
         :level,          :int,
         :_flags,         :uint32, # bit_fields
@@ -375,24 +391,32 @@ module HTS
         :line_skip,      :int32
     end
 
-    class Tbx < FFI::Struct
+    class Tbx < FFI::ManagedStruct
       layout \
-        :conf,           TbxConf.ptr,
+        :conf,           TbxConf,
         :idx,            HtsIdx.ptr,
         :dict,           :pointer
+
+      def self.release(ptr)
+        LibHTS.tbx_destroy(ptr) unless ptr.null?
+      end
     end
 
     # faidx
 
     FaiFormatOptions = enum(:FAI_NONE, :FAI_FASTA, :FAI_FASTQ)
 
-    class Faidx < FFI::Struct
-      layout :bgzf,      BGZF,
+    class Faidx < FFI::Struct # FIXME: ManagedStruct
+      layout :bgzf,      BGZF.ptr,
              :n,         :int,
              :m,         :int,
              :name,      :pointer,
              :hash,      :pointer,
              :format,    FaiFormatOptions
+
+      def self.release(ptr)
+        LibHTS.fai_destroy(ptr) unless ptr.null?
+      end
     end
 
     # bcf
@@ -404,7 +428,7 @@ module HTS
     end
 
     # Complete textual representation of a header line
-    class BcfHrec < FFI::Struct
+    class BcfHrec < FFI::ManagedStruct
       layout \
         :type,           :int,
         :key,            :string,
@@ -412,6 +436,10 @@ module HTS
         :nkeys,          :int,
         :keys,           :pointer,
         :vals,           :pointer
+
+      def self.release(ptr)
+        LibHTS.bcf_hrec_destroy(ptr) unless ptr.null?
+      end
     end
 
     class BcfInfo < FFI::BitStruct
@@ -435,7 +463,7 @@ module HTS
 
     class BcfIdinfo < FFI::Struct
       layout \
-        :info,           [:uint64_t, 3],
+        :info,           [:uint64, 3],
         :hrec,           [BcfHrec.ptr, 3],
         :id,             :int
     end
@@ -446,7 +474,7 @@ module HTS
         :val,            BcfIdinfo.ptr
     end
 
-    class BcfHdr < FFI::Struct
+    class BcfHdr < FFI::ManagedStruct
       layout \
         :n,              [:int, 3],
         :id,             [:pointer, 3], # BcfIdpair.ptr
@@ -461,6 +489,10 @@ module HTS
         :keep_samples,   :pointer,
         :mem,            KString,
         :m,              [:int, 3]
+
+      def self.release(ptr)
+        LibHTS.bcf_hdr_destroy(ptr) unless ptr.null?
+      end
     end
 
     class BcfFmt < FFI::BitStruct
@@ -504,7 +536,7 @@ module HTS
       layout \
         :pos,            :hts_pos_t,
         :rlen,           :hts_pos_t,
-        :rid,            :int32_t,
+        :rid,            :int32,
         :qual,           :float,
         :_n_info_allele, :uint32,
         :_n_fmt_sample,  :uint32,

data/lib/hts/libhts/cram.rb

@@ -352,7 +352,7 @@ module HTS
     # As int32_decoded/encode, but from/to blocks instead of cram_fd
     attach_function \
       :int32_put_blk,
-      %i[cram_block int32_t],
+      %i[cram_block int32],
       :int
 
     # Returns the refs_t structure used by a cram file handle.

data/lib/hts/libhts/sam.rb

@@ -242,13 +242,13 @@ module HTS
       [Bam1,
        :size_t,
        :string,
-       :uint16_t,
-       :int32_t,
+       :uint16,
+       :int32,
        :hts_pos_t,
-       :uint8_t,
+       :uint8,
        :size_t,
        :string,
-       :int32_t,
+       :int32,
        :hts_pos_t,
        :hts_pos_t,
        :size_t,

data/lib/hts/libhts/tbx.rb

@@ -68,3 +68,5 @@ module HTS
       :void
   end
 end
+
+require_relative "tbx_funcs"

data/lib/hts/libhts/tbx_funcs.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module HTS
   module LibHTS
     class << self
@@ -6,7 +8,7 @@ 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_, @@tbx_readrec)
       end
 
       def tbx_itr_querys(tbx, s)

data/lib/hts/libhts/vcf.rb

@@ -469,7 +469,7 @@ module HTS
     attach_function \
       :bcf_fmt_sized_array,
       [KString, :pointer],
-      :uint8_t
+      :uint8
 
     # Encode a variable-length char array in BCF format
     attach_function \

data/lib/hts/libhts/vcf_funcs.rb

@@ -294,15 +294,23 @@ module HTS
       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
+      # INT8_MIN  + 1
+      def bcf_int8_vector_end  = -127
+      # INT16_MIN + 1
+      def bcf_int16_vector_end = -32_767
+      # INT32_MIN + 1
+      def bcf_int32_vector_end = -2_147_483_647
+      # INT64_MIN + 1
+      def bcf_int64_vector_end = -9_223_372_036_854_775_807
       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
+      # INT8_MIN
+      def bcf_int8_missing     = -128
+      # INT16_MIN
+      def bcf_int16_missing    = (-32_767 - 1)
+      # INT32_MIN
+      def bcf_int32_missing    = (-2_147_483_647 - 1)
+      # INT64_MIN
+      def bcf_int64_missing    = (-9_223_372_036_854_775_807 - 1)
       def bcf_str_missing      = 0x07
 
       BCF_MAX_BT_INT8  = 0x7f           # INT8_MAX  */

data/lib/hts/tbx.rb

@@ -45,8 +45,6 @@ module HTS
 
       # build_index(index) if build_index
       @idx = load_index(index)
-
-      super # do nothing
     end
 
     def build_index
@@ -61,6 +59,10 @@ module HTS
       end
     end
 
+    def index_loaded?
+      !@idx.null?
+    end
+
     def tid(name)
       LibHTS.tbx_name2id(@idx, name)
     end
@@ -68,10 +70,53 @@ module HTS
     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
+        pts.read_array_of_pointer(nseq.read_int).map(&:read_string)
+      end
+    end
+
+    def query(region, start = nil, end_ = nil, &block)
+      check_closed
+      raise "Index file is required to call the query method." unless index_loaded?
+
+      if start && end_
+        queryi(tid(region), start, end_, &block)
+      else
+        querys(region, &block)
+      end
+    end
+
+    private
+
+    def queryi(id, start, end_)
+      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
+      self
+    end
+
+    def querys(region)
+      return to_enum(__method__, region) unless block_given?
+
+      qiter = LibHTS.tbx_itr_querys(@idx, region)
+
+      raise "Failed to query region: #{region}" if qiter.null?
+
+      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 = "0.2.3"
+  VERSION = "0.2.6"
 end

data/lib/htslib.rb

@@ -52,6 +52,7 @@ module HTS
   # before calling the LibHTS module.
   autoload :LibHTS, "hts/libhts"
 
+  autoload :Hts,    "hts/hts"
   autoload :Bam,    "hts/bam"
   autoload :Bcf,    "hts/bcf"
   autoload :Tbx,    "hts/tbx"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.3
+  version: 0.2.6
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-09-03 00:00:00.000000000 Z
+date: 2023-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -131,11 +131,13 @@ extra_rdoc_files: []
 files:
 - LICENSE.txt
 - README.md
+- TUTORIAL.md
 - lib/hts/bam.rb
 - lib/hts/bam/auxi.rb
 - lib/hts/bam/cigar.rb
 - lib/hts/bam/flag.rb
 - lib/hts/bam/header.rb
+- lib/hts/bam/header_record.rb
 - lib/hts/bam/record.rb
 - lib/hts/bcf.rb
 - lib/hts/bcf/format.rb
@@ -144,6 +146,7 @@ files:
 - lib/hts/bcf/info.rb
 - lib/hts/bcf/record.rb
 - lib/hts/faidx.rb
+- lib/hts/faidx/sequence.rb
 - lib/hts/ffi_ext/README.md
 - lib/hts/ffi_ext/pointer.rb
 - lib/hts/ffi_ext/struct.rb
@@ -186,7 +189,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.7
+rubygems_version: 3.4.1
 signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby