htslib 0.0.1 → 0.0.5

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

@@ -1,24 +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
+      layout \
+        :name,           KString,
+        :comment,        KString,
+        :seq,            KString,
+        :qual,           KString,
+        :last_char,      :int,
+        :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,
@@ -34,9 +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
@@ -95,7 +125,7 @@ module HTS
       :HTS_OPT_BLOCK_SIZE
     )
 
-    class HtsFormat < ::FFI::Struct
+    class HtsFormat < FFI::Struct
       layout \
         :category,          HtsFormatCategory,
         :format,            HtsExactFormat,
@@ -109,7 +139,7 @@ module HTS
         :specific,          :pointer
     end
 
-    class HtsIdx < ::FFI::Struct
+    class HtsIdx < FFI::Struct
       layout \
         :fmt,            :int,
         :min_shift,      :int,
@@ -142,7 +172,7 @@ module HTS
     end
 
     # HtsFile
-    class SamHdr < ::FFI::Struct
+    class SamHdr < FFI::Struct
       layout \
         :n_targets,      :int32,
         :ignore_sam_err, :int32,
@@ -158,11 +188,11 @@ module HTS
 
     BamHdr = SamHdr
 
-    class HtsFile < ::FFI::Struct
+    class HtsFile < FFI::BitStruct
       layout \
-        :bitfields,      :uint32, # FIXME
+        :_flags,         :uint32, # bit_fields
         :lineno,         :int64,
-        :line,           Kstring,
+        :line,           KString,
         :fn,             :string,
         :fn_aux,         :string,
         :fp,
@@ -176,17 +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,
@@ -198,9 +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,
@@ -225,9 +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,
@@ -243,53 +289,54 @@ module HTS
         :isize,          :hts_pos_t
     end
 
-    class Bam1 < ::FFI::Struct
+    class Bam1 < FFI::ManagedStruct
       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
+
+      def self.release(ptr)
+        LibHTS.bam_destroy1(ptr) unless ptr.null?
+      end
     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
 
-    BAM_CMATCH     = 0
-    BAM_CINS       = 1
-    BAM_CDEL       = 2
-    BAM_CREF_SKIP  = 3
-    BAM_CSOFT_CLIP = 4
-    BAM_CHARD_CLIP = 5
-    BAM_CPAD       = 6
-    BAM_CEQUAL     = 7
-    BAM_CDIFF      = 8
-    BAM_CBACK      = 9
-
-    BAM_CIGAR_STR = 'MIDNSHP=XB'
-    BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'
-    BAM_CIGAR_SHIFT = 4
-    BAM_CIGAR_MASK  = 0xf
-    BAM_CIGAR_TYPE  = 0x3C1A7
-
-    BAM_FPAIRED        =    1
-    BAM_FPROPER_PAIR   =    2
-    BAM_FUNMAP         =    4
-    BAM_FMUNMAP        =    8
-    BAM_FREVERSE       =   16
-    BAM_FMREVERSE      =   32
-    BAM_FREAD1         =   64
-    BAM_FREAD2         =  128
-    BAM_FSECONDARY     =  256
-    BAM_FQCFAIL        =  512
-    BAM_FDUP           = 1024
-    BAM_FSUPPLEMENTARY = 2048
-
-    class TbxConf < ::FFI::Struct
+    class TbxConf < FFI::Struct
       layout \
         :preset,         :int32,
         :sc,             :int32,
@@ -299,7 +346,7 @@ module HTS
         :line_skip,      :int32
     end
 
-    class Tbx < ::FFI::Struct
+    class Tbx < FFI::Struct
       layout \
         :conf,           TbxConf.ptr,
         :idx,            HtsIdx.ptr,
@@ -310,7 +357,7 @@ 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,
@@ -319,15 +366,15 @@ module HTS
              :format,    FaiFormatOptions
     end
 
-    # vcf
+    # bcf
 
-    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,
@@ -337,7 +384,7 @@ module HTS
         :vals,           :pointer
     end
 
-    class BcfFmt < ::FFI::Struct
+    class BcfFmt < FFI::BitStruct
       layout \
         :id,             :int,
         :n,              :int,
@@ -345,10 +392,14 @@ 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,
@@ -359,41 +410,45 @@ 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],
+        :info,           [:uint64_t, 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],
+        :id,             [:pointer, 3], # BcfIdpair.ptr
         :dict,           [:pointer, 3],
         :samples,        :pointer,
         :hrec,           :pointer,
         :nhrec,          :int,
         :dirty,          :int,
         :ntransl,        :int,
-        :transl,         :pointer,
+        :transl,         [:pointer, 2],
         :nsamples_ori,   :int,
         :keep_samples,   :pointer,
-        :mem,            Kstring,
+        :mem,            KString,
         :m,              [:int, 3]
     end
 
-    class BcfDec < ::FFI::Struct
+    class BcfDec < FFI::Struct
       layout \
         :m_fmt,          :int,
         :m_info,         :int,
@@ -401,34 +456,47 @@ module HTS
         :m_als,          :int,
         :m_allele,       :int,
         :m_flt,          :int,
+        :n_flt,          :int,
         :flt,            :pointer,
         :id,             :string,
-        :als,            :string,
+        :als,            :pointer, # (\\0-separated string)
         :allele,         :pointer,
-        :info,           BcfInfo.ptr,
+        :info,           :pointer, # 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::Struct
+    class Bcf1 < FFI::ManagedBitStruct
       layout \
         :pos,            :hts_pos_t,
         :rlen,           :hts_pos_t,
-        :rid,            :int,
+        :rid,            :int32_t,
         :qual,           :float,
-        :piyo,           :int, # FIXME
-        :fuga,           :int, # FIXME
-        :shared,         Kstring,
-        :indiv,          Kstring,
+        :_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
+
+      def self.release(ptr)
+        LibHTS.bcf_destroy(ptr) unless ptr.null?
+      end
     end
   end
 end

data/lib/hts/{ffi → libhts}/faidx.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # Build index for a FASTA or FASTQ or bgzip-compressed FASTA or FASTQ file.
     attach_function \
       :fai_build3,

data/lib/hts/{ffi → libhts}/hfile.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # Open the named file or URL as a stream
     attach_function \
       :hopen,
@@ -23,7 +23,7 @@ module HTS
     # Append an extension or replace an existing extension
     attach_function \
       :haddextension,
-      [Kstring, :string, :int, :string],
+      [KString, :string, :int, :string],
       :string
 
     # Flush (for output streams) and close the stream

data/lib/hts/{ffi → libhts}/hts.rb

@@ -1,14 +1,20 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # hts_expand
     # hts_expand3
     # hts_resize
 
+    # hts_log.h
+    attach_function \
+      :hts_get_log_level,
+      [],
+      HtsLogLevel
+
     attach_function \
       :hts_lib_shutdown,
-      [:void],
+      [],
       :void
 
     attach_function \
@@ -110,7 +116,7 @@ module HTS
     # Read a line (and its \n or \r\n terminator) from a file
     attach_function \
       :hts_getline,
-      [HtsFile, :int, Kstring],
+      [HtsFile, :int, KString],
       :int
 
     attach_function \

data/lib/hts/{ffi → libhts}/kfunc.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # Log gamma function
     attach_function \
       :kf_lgamma,