htslib 0.0.2 → 0.0.3

data/lib/hts/fai.rb

@@ -18,30 +18,30 @@ module HTS
 
     def initialize(path)
       @path = File.expand_path(path)
-      @path.delete_suffix!('.fai')
-      FFI.fai_build(@path) unless File.exist?("#{@path}.fai")
-      @fai = FFI.fai_load(@path)
+      @path.delete_suffix!(".fai")
+      LibHTS.fai_build(@path) unless File.exist?("#{@path}.fai")
+      @fai = LibHTS.fai_load(@path)
       raise if @fai.null?
 
-      # at_exit{FFI.fai_destroy(@fai)}
+      # at_exit{LibHTS.fai_destroy(@fai)}
     end
 
     def close
-      FFI.fai_destroy(@fai)
+      LibHTS.fai_destroy(@fai)
     end
 
     # the number of sequences in the index.
     def size
-      FFI.faidx_nseq(@fai)
+      LibHTS.faidx_nseq(@fai)
     end
     alias length size
 
     # return the length of the requested chromosome.
     def chrom_size(chrom)
-      raise ArgumentError, 'Expect chrom to be String or Symbol' unless chrom.is_a?(String) || chrom.is_a?(Symbol)
+      raise ArgumentError, "Expect chrom to be String or Symbol" unless chrom.is_a?(String) || chrom.is_a?(Symbol)
 
       chrom = chrom.to_s
-      result = FFI.faidx_seq_len(@fai, chrom)
+      result = LibHTS.faidx_seq_len(@fai, chrom)
       result == -1 ? nil : result
     end
     alias chrom_length chrom_size

data/lib/hts/libhts.rb

@@ -0,0 +1,141 @@
+# frozen_string_literal: true
+
+module HTS
+  module LibHTS
+    extend FFI::Library
+
+    begin
+      ffi_lib HTS.lib_path
+    rescue LoadError => e
+      raise LoadError, "#{e}\nCould not find #{HTS.lib_path}"
+    end
+
+    def self.attach_function(*)
+      super
+    rescue FFI::NotFoundError => e
+      warn e.message
+    end
+  end
+end
+
+module FFI
+  class Struct
+    class << self
+      # @example HtsOpt
+      #   class HtsOpt < FFI::Struct
+      #     layout \
+      #       :arg,            :string,
+      #       :opt,            HtsFmtOption,
+      #       :val,
+      #       union_layout(
+      #         :i,            :int,
+      #         :s,            :string
+      #       ),
+      #       :next,           HtsOpt.ptr
+      #   end
+
+      def union_layout(*args)
+        Class.new(FFI::Union) { layout(*args) }
+      end
+
+      # @example HtsFormat
+      #   class HtsFormat < FFI::Struct
+      #     layout \
+      #       :category,          HtsFormatCategory,
+      #       :format,            HtsExactFormat,
+      #       :version,
+      #       struct_layout(
+      #         :major,           :short,
+      #         :minor,           :short
+      #       ),
+      #       :compression,       HtsCompression,
+      #       :compression_level, :short,
+      #       :specific,          :pointer
+      #   end
+
+      def struct_layout(*args)
+        Class.new(FFI::Struct) { layout(*args) }
+      end
+    end
+  end
+
+  # Struct that support bit fields.
+  # Currently readonly.
+  class BitStruct < Struct
+    class << self
+      module BitFieldsModule
+        def [](name)
+          bit_fields = self.class.bit_fields_hash_table
+          parent, start, width = bit_fields[name]
+          if parent
+            (super(parent) >> start) & ((1 << width) - 1)
+          else
+            super(name)
+          end
+        end
+      end
+      private_constant :BitFieldsModule
+
+      attr_reader :bit_fields_hash_table
+
+      # @example Bcf1
+      #   class Bcf1 < FFI::BitStruct
+      #     layout \
+      #       :pos,            :hts_pos_t,
+      #       :rlen,           :hts_pos_t,
+      #       :rid,            :int32_t,
+      #       :qual,           :float,
+      #       :_n_info_allele, :uint32_t,
+      #       :_n_fmt_sample,  :uint32_t,
+      #       :shared,         KString,
+      #       :indiv,          KString,
+      #       :d,              BcfDec,
+      #       :max_unpack,     :int,
+      #       :unpacked,       :int,
+      #       :unpack_size,    [:int, 3],
+      #       :errcode,        :int
+      #
+      #     bit_fields :_n_info_allele,
+      #                :n_info,   16,
+      #                :n_allele, 16
+      #
+      #     bit_fields :_n_fmt_sample,
+      #                :n_fmt,    8,
+      #                :n_sample, 24
+      #   end
+
+      def bit_fields(*args)
+        unless instance_variable_defined?(:@bit_fields_hash_table)
+          @bit_fields_hash_table = {}
+          prepend BitFieldsModule
+        end
+
+        parent = args.shift
+        labels = []
+        widths = []
+        args.each_slice(2) do |l, w|
+          labels << l
+          widths << w
+        end
+        starts = widths.inject([0]) do |result, w|
+          result << (result.last + w)
+        end
+        labels.zip(starts, widths).each do |l, s, w|
+          @bit_fields_hash_table[l] = [parent, s, w]
+        end
+      end
+    end
+  end
+end
+
+require_relative "libhts/constants"
+
+# alphabetical order
+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/vcf"

data/lib/hts/{ffi → libhts}/bgzf.rb

@@ -2,7 +2,7 @@
 
 # BGZF
 module HTS
-  module FFI
+  module LibHTS
     # Open an existing file descriptor for reading or writing.
     attach_function \
       :bgzf_dopen,

data/lib/hts/{ffi → libhts}/constants.rb

@@ -1,34 +1,34 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     typedef :pointer, :HFILE
     typedef :int64, :hts_pos_t
     typedef :pointer, :bam_plp_auto_f
 
     # kstring
 
-    class KString < ::FFI::Struct
+    class KString < FFI::Struct
       layout \
         :l,              :size_t,
         :m,              :size_t,
         :s,              :string
     end
 
-    class KSeq < ::FFI::Struct
+    class KSeq < FFI::Struct
       layout \
         :name,           KString,
         :comment,        KString,
         :seq,            KString,
         :qual,           KString,
         :last_char,      :int,
-        :f,              :pointer # FIXME
+        :f,              :pointer # kstream_t
     end
 
     # BGZF
-    class BGZF < ::FFI::Struct
+    class BGZF < FFI::BitStruct
       layout \
-        :piyo1,                  :uint, # FIXME
+        :_flags,                 :uint, # bit_fields
         :cache_size,             :int,
         :block_length,           :int,
         :block_clength,          :int,
@@ -44,9 +44,29 @@ module HTS
         :idx_build_otf,          :int,
         :gz_stream,              :pointer,
         :seeked,                 :int64
+
+      bit_fields :_flags,
+                 :errcode,        16,
+                 :_reserved,      1,
+                 :is_write,       1,
+                 :no_eof_block,   1,
+                 :is_be,          1,
+                 :compress_level, 9,
+                 :last_block_eof, 1,
+                 :is_compressed,  1,
+                 :is_gzip,        1
     end
 
     # hts
+    HtsLogLevel = enum(
+      :off,            # All logging disabled.
+      :error,          # Logging of errors only.
+      :warning, 3,     # Logging of errors and warnings.
+      :info,           # Logging of errors, warnings, and normal but significant events.
+      :debug,          # Logging of all except the most detailed debug events.
+      :trace           # All logging enabled.
+    )
+
     HtsFormatCategory = enum(
       :unknown_category,
       :sequence_data,    # Sequence data -- SAM, BAM, CRAM, etc
@@ -105,7 +125,7 @@ module HTS
       :HTS_OPT_BLOCK_SIZE
     )
 
-    class HtsFormat < ::FFI::Struct
+    class HtsFormat < FFI::Struct
       layout \
         :category,          HtsFormatCategory,
         :format,            HtsExactFormat,
@@ -119,7 +139,7 @@ module HTS
         :specific,          :pointer
     end
 
-    class HtsIdx < ::FFI::Struct
+    class HtsIdx < FFI::Struct
       layout \
         :fmt,            :int,
         :min_shift,      :int,
@@ -152,7 +172,7 @@ module HTS
     end
 
     # HtsFile
-    class SamHdr < ::FFI::Struct
+    class SamHdr < FFI::Struct
       layout \
         :n_targets,      :int32,
         :ignore_sam_err, :int32,
@@ -168,9 +188,9 @@ module HTS
 
     BamHdr = SamHdr
 
-    class HtsFile < ::FFI::Struct
+    class HtsFile < FFI::BitStruct
       layout \
-        :bitfields,      :uint32, # FIXME
+        :_flags,         :uint32, # bit_fields
         :lineno,         :int64,
         :line,           KString,
         :fn,             :string,
@@ -186,17 +206,25 @@ module HTS
         :idx,            HtsIdx.ptr,
         :fnidx,          :string,
         :bam_header,     SamHdr.ptr
+
+      bit_fields :_flags,
+                 :is_bin,         1,
+                 :is_write,       1,
+                 :is_be,          1,
+                 :is_cram,        1,
+                 :is_bgzf,        1,
+                 :dummy,          27
     end
 
     SamFile = HtsFile
 
-    class HtsThreadPool < ::FFI::Struct
+    class HtsThreadPool < FFI::Struct
       layout \
         :pool,           :pointer,
         :qsize,          :int
     end
 
-    class HtsOpt < ::FFI::Struct
+    class HtsOpt < FFI::Struct
       layout \
         :arg,            :string,
         :opt,            HtsFmtOption,
@@ -208,9 +236,9 @@ module HTS
         :next,           HtsOpt.ptr
     end
 
-    class HtsItr < ::FFI::Struct
+    class HtsItr < FFI::BitStruct
       layout \
-        :foo,            :uint32, # FIXME
+        :_flags,         :uint32, # bit_fields
         :tid,            :int,
         :n_off,          :int,
         :i,              :int,
@@ -235,9 +263,17 @@ module HTS
           :m,            :int,
           :a,            :pointer
         )
+
+      bit_fields :_flags,
+                 :read_rest, 1,
+                 :finished,  1,
+                 :is_cram,   1,
+                 :nocoor,    1,
+                 :multi,     1,
+                 :dummy,     27
     end
 
-    class Bam1Core < ::FFI::Struct
+    class Bam1Core < FFI::Struct
       layout \
         :pos,            :hts_pos_t,
         :tid,            :int32,
@@ -253,23 +289,50 @@ module HTS
         :isize,          :hts_pos_t
     end
 
-    class Bam1 < ::FFI::Struct
+    class Bam1 < FFI::Struct
       layout \
         :core,           Bam1Core,
         :id,             :uint64,
         :data,           :pointer, # uint8_t
         :l_data,         :int,
         :m_data,         :uint32,
-        :mempolicy,      :uint32
+        :_mempolicy,     :uint32 # bit_fields
+
+      # bit_fields :_mempolicy,
+      #            :mempolicy,  2,
+      #            :_reserved,  30
     end
 
-    class BamPlp < ::FFI::Struct
+    typedef :pointer, :bam_plp
+    typedef :pointer, :bam_mplp
+
+    class BamPileupCd < FFI::Union
+      layout \
+        :p,               :pointer,
+        :i,               :int64_t,
+        :f,               :double
     end
 
-    class BamMplp < ::FFI::Struct
+    class BamPileup1 < FFI::BitStruct
+      layout \
+        :b,              Bam1.ptr,
+        :qpos,           :int32_t,
+        :indel,          :int,
+        :level,          :int,
+        :_flags,         :uint32_t, # bit_fields
+        :cd,             BamPileupCd,
+        :cigar_ind,      :int
+
+      bit_fields :_flags,
+                 :is_del,     1,
+                 :is_head,    1,
+                 :is_tail,    1,
+                 :is_refskip, 1,
+                 :_reserved,  1,
+                 :aux,        27
     end
 
-    class TbxConf < ::FFI::Struct
+    class TbxConf < FFI::Struct
       layout \
         :preset,         :int32,
         :sc,             :int32,
@@ -279,7 +342,7 @@ module HTS
         :line_skip,      :int32
     end
 
-    class Tbx < ::FFI::Struct
+    class Tbx < FFI::Struct
       layout \
         :conf,           TbxConf.ptr,
         :idx,            HtsIdx.ptr,
@@ -290,7 +353,7 @@ module HTS
 
     FaiFormatOptions = enum(:FAI_NONE, :FAI_FASTA, :FAI_FASTQ)
 
-    class Faidx < ::FFI::Struct
+    class Faidx < FFI::Struct
       layout :bgzf,      BGZF,
              :n,         :int,
              :m,         :int,
@@ -301,13 +364,13 @@ module HTS
 
     # vcf
 
-    class Variant < ::FFI::Struct
+    class BcfVariant < FFI::Struct
       layout \
         :type,           :int,
         :n,              :int
     end
 
-    class BcfHrec < ::FFI::Struct
+    class BcfHrec < FFI::Struct
       layout \
         :type,           :int,
         :key,            :string,
@@ -317,7 +380,7 @@ module HTS
         :vals,           :pointer
     end
 
-    class BcfFmt < ::FFI::Struct
+    class BcfFmt < FFI::BitStruct
       layout \
         :id,             :int,
         :n,              :int,
@@ -325,10 +388,14 @@ module HTS
         :type,           :int,
         :p,              :pointer, # uint8_t
         :p_len,          :uint32,
-        :piyo,           :uint32 # FIXME
+        :_p_off_free,    :uint32 # bit_fields
+
+      bit_fields :_p_off_free,
+                 :p_off,  31,
+                 :p_free, 1
     end
 
-    class BcfInfo < ::FFI::Struct
+    class BcfInfo < FFI::BitStruct
       layout \
         :key,            :int,
         :type,           :int,
@@ -339,24 +406,28 @@ module HTS
         ),
         :vptr,           :pointer,
         :vptr_len,       :uint32,
-        :piyo,           :uint32, # FIXME
+        :_vptr_off_free, :uint32, # bit_fields
         :len,            :int
+
+      bit_fields :_vptr_off_free,
+                 :vptr_off, 31,
+                 :vptr_free, 1
     end
 
-    class BcfIdinfo < ::FFI::Struct
+    class BcfIdinfo < FFI::Struct
       layout \
         :info,           [:uint8, 3],
         :hrec,           [BcfHrec.ptr, 3],
         :id,             :int
     end
 
-    class BcfIdpair < ::FFI::Struct
+    class BcfIdpair < FFI::Struct
       layout \
         :key,            :string,
         :val,            BcfIdinfo.ptr
     end
 
-    class BcfHdr < ::FFI::Struct
+    class BcfHdr < FFI::Struct
       layout \
         :n,              [:int, 3],
         :id,             [BcfIdpair.ptr, 3],
@@ -373,7 +444,7 @@ module HTS
         :m,              [:int, 3]
     end
 
-    class BcfDec < ::FFI::Struct
+    class BcfDec < FFI::Struct
       layout \
         :m_fmt,          :int,
         :m_info,         :int,
@@ -388,21 +459,21 @@ module HTS
         :allele,         :pointer,
         :info,           BcfInfo.ptr,
         :fmt,            BcfFmt.ptr,
-        :var,            Variant.ptr,
+        :var,            BcfVariant.ptr,
         :n_var,          :int,
         :var_type,       :int,
         :shared_dirty,   :int,
         :indiv_dirty,    :int
     end
 
-    class Bcf1 < ::FFI::BitStruct
+    class Bcf1 < FFI::BitStruct
       layout \
         :pos,            :hts_pos_t,
         :rlen,           :hts_pos_t,
         :rid,            :int32_t,
         :qual,           :float,
-        :n_info_allele,  :uint32_t, # FIXME
-        :n_fmt_sample,   :uint32_t, # FIXME
+        :_n_info_allele, :uint32_t,
+        :_n_fmt_sample,  :uint32_t,
         :shared,         KString,
         :indiv,          KString,
         :d,              BcfDec,
@@ -411,13 +482,13 @@ module HTS
         :unpack_size,    [:int, 3],
         :errcode,        :int
 
-      bitfields :n_info_allele,
-                :n_info,   16,
-                :n_allele, 16
+      bit_fields :_n_info_allele,
+                 :n_info,   16,
+                 :n_allele, 16
 
-      bitfields :n_fmt_sample,
-                :n_fmt,    8,
-                :n_sample, 24
+      bit_fields :_n_fmt_sample,
+                 :n_fmt,    8,
+                 :n_sample, 24
     end
   end
 end