htslib 0.0.2 → 0.0.6

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 +289,54 @@ 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
 
-    class TbxConf < ::FFI::Struct
+    class TbxConf < FFI::Struct
       layout \
         :preset,         :int32,
         :sc,             :int32,
@@ -279,7 +346,7 @@ module HTS
         :line_skip,      :int32
     end
 
-    class Tbx < ::FFI::Struct
+    class Tbx < FFI::Struct
       layout \
         :conf,           TbxConf.ptr,
         :idx,            HtsIdx.ptr,
@@ -290,7 +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,
@@ -299,15 +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,
@@ -317,7 +384,7 @@ module HTS
         :vals,           :pointer
     end
 
-    class BcfFmt < ::FFI::Struct
+    class BcfFmt < FFI::BitStruct
       layout \
         :id,             :int,
         :n,              :int,
@@ -325,10 +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,
@@ -339,27 +410,31 @@ 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,
@@ -373,7 +448,7 @@ module HTS
         :m,              [:int, 3]
     end
 
-    class BcfDec < ::FFI::Struct
+    class BcfDec < FFI::Struct
       layout \
         :m_fmt,          :int,
         :m_info,         :int,
@@ -386,23 +461,23 @@ module HTS
         :id,             :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::BitStruct
+    class Bcf1 < FFI::ManagedBitStruct
       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 +486,17 @@ 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
+
+      bit_fields :_n_fmt_sample,
+                 :n_fmt,    8,
+                 :n_sample, 24
 
-      bitfields :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,

data/lib/hts/{ffi → libhts}/hts.rb

@@ -1,11 +1,17 @@
 # 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,
       [],
@@ -83,6 +89,12 @@ module HTS
       %i[HFILE string string],
       HtsFile.by_ref
 
+    # For output streams, flush any buffered data
+    attach_function \
+      :hts_flush,
+      [HtsFile],
+      :int
+
     # Close a file handle, flushing buffered data for output streams
     attach_function \
       :hts_close,

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,

data/lib/hts/libhts/sam.rb

@@ -0,0 +1,102 @@
+# frozen_string_literal: true
+
+require_relative "sam_funcs"
+
+module HTS
+  module LibHTS
+    # constants
+    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_SHIFT = 4
+    BAM_CIGAR_MASK  = 0xf
+    BAM_CIGAR_TYPE  = 0x3C1A7
+
+    # macros
+    class << self
+      def bam_cigar_op(c)
+        c & BAM_CIGAR_MASK
+      end
+
+      def bam_cigar_oplen(c)
+        c >> BAM_CIGAR_SHIFT
+      end
+
+      def bam_cigar_opchr(c)
+        ("#{BAM_CIGAR_STR}??????")[bam_cigar_op(c)]
+      end
+
+      def bam_cigar_gen(l, o)
+        l << BAM_CIGAR_SHIFT | o
+      end
+
+      def bam_cigar_type(o)
+        BAM_CIGAR_TYPE >> (o << 1) & 3
+      end
+    end
+
+    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
+
+    # macros
+    # function-like macros
+    class << self
+      def bam_is_rev(b)
+        b[:core][:flag] & BAM_FREVERSE != 0
+      end
+
+      def bam_is_mrev(b)
+        b[:core][:flag] & BAM_FMREVERSE != 0
+      end
+
+      def bam_get_qname(b)
+        b[:data]
+      end
+
+      def bam_get_cigar(b)
+        b[:data] + b[:core][:l_qname]
+      end
+
+      def bam_get_seq(b)
+        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname]
+      end
+
+      def bam_get_qual(b)
+        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] + ((b[:core][:l_qseq] + 1) >> 1)
+      end
+
+      def bam_get_aux(b)
+        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] + ((b[:core][:l_qseq] + 1) >> 1) + b[:core][:l_qseq]
+      end
+
+      def bam_get_l_aux(b)
+        b[:l_data] - (b[:core][:n_cigar] << 2) - b[:core][:l_qname] - b[:core][:l_qseq] - ((b[:core][:l_qseq] + 1) >> 1)
+      end
+
+      def bam_seqi(s, i)
+        s[(i) >> 1].read_uint8 >> ((~i & 1) << 2) & 0xf
+      end
+
+      # def bam_set_seqi(s, i, b)
+    end
+  end
+end