htslib 0.0.0.pre

data/lib/hts/ffi/struct.rb

@@ -0,0 +1,12 @@
+# This should be removed if you get the better way...
+module FFI
+  class Struct
+    def self.union_layout(*args)
+      Class.new(FFI::Union) { layout(*args) }
+    end
+
+    def self.struct_layout(*args)
+      Class.new(FFI::Struct) { layout(*args) }
+    end
+  end
+end

data/lib/hts/ffi/tbx.rb

@@ -0,0 +1,68 @@
+module HTS
+  module FFI
+    attach_function \
+      :tbx_name2id,
+      [Tbx, :string],
+      :int
+
+    # Internal helper function used by tbx_itr_next()
+    attach_function \
+      :hts_get_bgzfp,
+      [HtsFile],
+      BGZF.by_ref
+
+    attach_function \
+      :tbx_readrec,
+      [BGZF, :pointer, :pointer, :pointer, :pointer, :pointer],
+      :int
+
+    # Build an index of the lines in a BGZF-compressed file
+    attach_function \
+      :tbx_index,
+      [BGZF, :int, TbxConf],
+      Tbx.by_ref
+
+    attach_function \
+      :tbx_index_build,
+      [:string, :int, TbxConf],
+      :int
+
+    attach_function \
+      :tbx_index_build2,
+      [:string, :string, :int, TbxConf],
+      :int
+
+    attach_function \
+      :tbx_index_build3,
+      [:string, :string, :int, :int, TbxConf],
+      :int
+
+    # Load or stream a .tbi or .csi index
+    attach_function \
+      :tbx_index_load,
+      [:string],
+      Tbx.by_ref
+
+    # Load or stream a .tbi or .csi index
+    attach_function \
+      :tbx_index_load2,
+      %i[string string],
+      Tbx.by_ref
+
+    # Load or stream a .tbi or .csi index
+    attach_function \
+      :tbx_index_load3,
+      %i[string string int],
+      Tbx.by_ref
+
+    attach_function \
+      :tbx_seqnames,
+      [Tbx, :int],
+      :pointer
+
+    attach_function \
+      :tbx_destroy,
+      [Tbx],
+      :void
+  end
+end

data/lib/hts/ffi_constants.rb

@@ -0,0 +1,430 @@
+module HTS
+  module FFI
+    typedef :pointer, :HFILE
+    typedef :int64, :hts_pos_t
+    typedef :pointer, :bam_plp_auto_f
+
+    # kstring
+
+    class Kstring < ::FFI::Struct
+      layout \
+        :l,              :size_t,
+        :m,              :size_t,
+        :s,              :string
+    end
+
+    # BGZF
+    class BGZF < ::FFI::Struct
+      layout \
+        :piyo1,                  :uint, # FIXME
+        :cache_size,             :int,
+        :block_length,           :int,
+        :block_clength,          :int,
+        :block_offset,           :int,
+        :block_address,          :int64,
+        :uncompressed_address,   :int64,
+        :uncompressed_block,     :pointer,
+        :compressed_block,       :pointer,
+        :cache,                  :pointer,
+        :fp,                     :HFILE,
+        :mt,                     :pointer,
+        :idx,                    :pointer,
+        :idx_build_otf,          :int,
+        :gz_stream,              :pointer,
+        :seeked,                 :int64
+    end
+
+    # hts
+    HtsFormatCategory = enum(
+      :unknown_category,
+      :sequence_data,    # Sequence data -- SAM, BAM, CRAM, etc
+      :variant_data,     # Variant calling data -- VCF, BCF, etc
+      :index_file,       # Index file associated with some data file
+      :region_list,      # Coordinate intervals or regions -- BED, etc
+      :category_maximum, 32_767
+    )
+
+    HtsExactFormat = enum(
+      :unknown_format,
+      :binary_format, :text_format,
+      :sam, :bam, :bai, :cram, :crai, :vcf, :bcf, :csi, :gzi, :tbi, :bed,
+      :htsget, :json,
+      :empty_format,
+      :fasta_format, :fastq_format, :fai_format, :fqi_format,
+      :hts_crypt4gh_format,
+      :format_maximum, 32_767
+    )
+
+    HtsCompression = enum(
+      :no_compression, :gzip, :bgzf, :custom,
+      :compression_maximum, 32_767
+    )
+
+    HtsFmtOption = enum(
+      :CRAM_OPT_DECODE_MD,
+      :CRAM_OPT_PREFIX,
+      :CRAM_OPT_VERBOSITY,   # obsolete, use hts_set_log_level() instead
+      :CRAM_OPT_SEQS_PER_SLICE,
+      :CRAM_OPT_SLICES_PER_CONTAINER,
+      :CRAM_OPT_RANGE,
+      :CRAM_OPT_VERSION,     # rename to :CRAM_version?
+      :CRAM_OPT_EMBED_REF,
+      :CRAM_OPT_IGNORE_MD5,
+      :CRAM_OPT_REFERENCE,   # make general
+      :CRAM_OPT_MULTI_SEQ_PER_SLICE,
+      :CRAM_OPT_NO_REF,
+      :CRAM_OPT_USE_BZIP2,
+      :CRAM_OPT_SHARED_REF,
+      :CRAM_OPT_NTHREADS,    # deprecated, use HTS_OPT_NTHREADS
+      :CRAM_OPT_THREAD_POOL, # make general
+      :CRAM_OPT_USE_LZMA,
+      :CRAM_OPT_USE_RANS,
+      :CRAM_OPT_REQUIRED_FIELDS,
+      :CRAM_OPT_LOSSY_NAMES,
+      :CRAM_OPT_BASES_PER_SLICE,
+      :CRAM_OPT_STORE_MD,
+      :CRAM_OPT_STORE_NM,
+      :CRAM_OPT_RANGE_NOSEEK, # CRAM_OPT_RANGE minus the seek
+      # General purpose
+      :HTS_OPT_COMPRESSION_LEVEL, 100,
+      :HTS_OPT_NTHREADS,
+      :HTS_OPT_THREAD_POOL,
+      :HTS_OPT_CACHE_SIZE,
+      :HTS_OPT_BLOCK_SIZE
+    )
+
+    class HtsFormat < ::FFI::Struct
+      layout \
+        :category,          HtsFormatCategory,
+        :format,            HtsExactFormat,
+        :version,
+        struct_layout(
+          :major,           :short,
+          :minor,           :short
+        ),
+        :compression,       HtsCompression,
+        :compression_level, :short,
+        :specific,          :pointer
+    end
+
+    class HtsIdx < ::FFI::Struct
+      layout \
+        :fmt,            :int,
+        :min_shift,      :int,
+        :n_lvls,         :int,
+        :n_bins,         :int,
+        :l_meta,         :uint32,
+        :n,              :int32,
+        :m,              :int32,
+        :n_no_coor,      :uint64,
+        :bidx,           :pointer,
+        :lidx,           :pointer,
+        :meta,           :pointer,
+        :tbi_n,          :int,
+        :last_tbi_tid,   :int,
+        :z,
+        union_layout(
+          :last_bin,     :uint32,
+          :save_bin,     :uint32,
+          :last_coor,    :pointer,
+          :last_tid,     :int,
+          :save_tid,     :int,
+          :finished,     :int,
+          :last_off,     :uint64,
+          :save_off,     :uint64,
+          :off_beg,      :uint64,
+          :off_end,      :uint64,
+          :n_mapped,     :uint64,
+          :n_unmapped,   :uint64
+        )
+    end
+
+    class SamHdr < ::FFI::Struct # HtsFile
+      layout \
+        :n_targets,      :int32,
+        :ignore_sam_err, :int32,
+        :l_text,         :size_t,
+        :target_len,     :pointer,
+        :cigar_tab,      :pointer,
+        :target_name,    :pointer,
+        :text,           :string,
+        :sdict,          :pointer,
+        :hrecs,          :pointer,
+        :ref_count,      :uint32
+    end
+
+    BamHdr = SamHdr
+
+    class HtsFile < ::FFI::Struct
+      layout \
+        :bitfields,      :uint32, # FIXME
+        :lineno,         :int64,
+        :line,           Kstring,
+        :fn,             :string,
+        :fn_aux,         :string,
+        :fp,
+        union_layout(
+          :bgzf,         BGZF.ptr,
+          :cram,         :pointer,
+          :hfile,        :pointer # HFILE
+        ),
+        :state,          :pointer,
+        :format,         HtsFormat,
+        :idx,            HtsIdx.ptr,
+        :fnidx,          :string,
+        :bam_header,     SamHdr.ptr
+    end
+
+    SamFile = HtsFile
+
+    class HtsThreadPool < ::FFI::Struct
+      layout \
+        :pool,           :pointer,
+        :qsize,          :int
+    end
+
+    class HtsOpt < ::FFI::Struct
+      layout \
+        :arg,            :string,
+        :opt,            HtsFmtOption,
+        :val,
+        union_layout(
+          :i,            :int,
+          :s,            :string
+        ),
+        :next,           HtsOpt.ptr
+    end
+
+    class HtsItr < ::FFI::Struct
+      layout \
+        :foo,            :uint32, # FIXME
+        :tid,            :int,
+        :n_off,          :int,
+        :i,              :int,
+        :n_reg,          :int,
+        :beg,            :int64,
+        :end,            :int64,
+        :reg_list,       :pointer,
+        :curr_tid,       :int,
+        :curr_reg,       :int,
+        :curr_intv,      :int,
+        :curr_beg,       :int64,
+        :curr_end,       :int64,
+        :curr_off,       :uint64,
+        :nocoor_off,     :uint64,
+        :off,            :pointer,
+        :readrec,        :pointer,
+        :seek,           :pointer,
+        :tell,           :pointer,
+        :bins,
+        union_layout(
+          :n,            :int,
+          :m,            :int,
+          :a,            :pointer
+        )
+    end
+    class Bam1Core < ::FFI::Struct
+      layout \
+        :pos,            :hts_pos_t,
+        :tid,            :int32,
+        :bin,            :uint16,
+        :qual,           :uint8,
+        :l_extranul,     :uint8,
+        :flag,           :uint16,
+        :l_qname,        :uint16,
+        :n_cigar,        :uint32,
+        :l_qseq,         :int32,
+        :mtid,           :int32,
+        :mpos,           :hts_pos_t,
+        :isize,          :hts_pos_t
+    end
+
+    class Bam1 < ::FFI::Struct
+      layout \
+        :core,           Bam1Core,
+        :id,             :uint64,
+        :data,           :pointer, # uint8_t
+        :l_data,         :int,
+        :m_data,         :uint32,
+        :mempolicy,      :uint32
+    end
+
+    class BamPlp < ::FFI::Struct
+    end
+
+    class BamMplp < ::FFI::Struct
+    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'.freeze
+    BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'.freeze
+    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
+      layout \
+        :preset,         :int32,
+        :sc,             :int32,
+        :bc,             :int32,
+        :ec,             :int32,
+        :meta_char,      :int32,
+        :line_skip,      :int32
+    end
+
+    class Tbx < ::FFI::Struct
+      layout \
+        :conf,           TbxConf.ptr,
+        :idx,            HtsIdx.ptr,
+        :dict,           :pointer
+    end
+
+    # faidx
+
+    FaiFormatOptions = enum(:FAI_NONE, :FAI_FASTA, :FAI_FASTQ)
+
+    class Faidx < ::FFI::Struct
+      layout :bgzf,      BGZF,
+             :n,         :int,
+             :m,         :int,
+             :name,      :pointer,
+             :hash,      :pointer,
+             :format,    FaiFormatOptions
+    end
+
+    # vcf
+
+    class Variant < ::FFI::Struct
+      layout \
+        :type,           :int,
+        :n,              :int
+    end
+
+    class BcfHrec < ::FFI::Struct
+      layout \
+        :type,           :int,
+        :key,            :string,
+        :value,          :string,
+        :nkeys,          :int,
+        :keys,           :pointer,
+        :vals,           :pointer
+    end
+
+    class BcfFmt < ::FFI::Struct
+      layout \
+        :id,             :int,
+        :n,              :int,
+        :size,           :int,
+        :type,           :int,
+        :p,              :pointer, # uint8_t
+        :p_len,          :uint32,
+        :piyo,           :uint32 # FIXME
+    end
+
+    class BcfInfo < ::FFI::Struct
+      layout \
+        :key,            :int,
+        :type,           :int,
+        :v1,
+        union_layout(
+          :i,            :int64,
+          :f,            :float
+        ),
+        :vptr,           :pointer,
+        :vptr_len,       :uint32,
+        :piyo,           :uint32, # FIXME
+        :len,            :int
+    end
+
+    class BcfIdinfo < ::FFI::Struct
+      layout \
+        :info,           [:uint8, 3],
+        :hrec,           [BcfHrec.ptr, 3],
+        :id,             :int
+    end
+
+    class BcfIdpair < ::FFI::Struct
+      layout \
+        :key,            :string,
+        :val,            BcfIdinfo.ptr
+    end
+
+    class BcfHdr < ::FFI::Struct
+      layout \
+        :n,              [:int, 3],
+        :id,             [BcfIdpair.ptr, 3],
+        :dict,           [:pointer, 3],
+        :samples,        :pointer,
+        :hrec,           :pointer,
+        :nhrec,          :int,
+        :dirty,          :int,
+        :ntransl,        :int,
+        :transl,         :pointer,
+        :nsamples_ori,   :int,
+        :keep_samples,   :pointer,
+        :mem,            Kstring,
+        :m,              [:int, 3]
+    end
+
+    class BcfDec < ::FFI::Struct
+      layout \
+        :m_fmt,          :int,
+        :m_info,         :int,
+        :m_id,           :int,
+        :m_als,          :int,
+        :m_allele,       :int,
+        :m_flt,          :int,
+        :flt,            :pointer,
+        :id,             :string,
+        :als,            :string,
+        :allele,         :pointer,
+        :info,           BcfInfo.ptr,
+        :fmt,            BcfFmt.ptr,
+        :var,            Variant.ptr,
+        :n_var,          :int,
+        :var_type,       :int,
+        :shared_dirty,   :int,
+        :indiv_dirty,    :int
+    end
+
+    class Bcf1 < ::FFI::Struct
+      layout \
+        :pos,            :hts_pos_t,
+        :rlen,           :hts_pos_t,
+        :rid,            :int,
+        :qual,           :float,
+        :piyo,           :int, # FIXME
+        :fuga,           :int, # FIXME
+        :shared,         Kstring,
+        :indiv,          Kstring,
+        :d,              BcfDec,
+        :max_unpack,     :int,
+        :unpacked,       :int,
+        :unpack_size,    [:int, 3],
+        :errcode,        :int
+    end
+  end
+end