htslib 0.4.1 → 0.5.0

data/lib/hts/libhts/cram.rb

@@ -1,471 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    typedef :pointer, :cram_fd
-    typedef :pointer, :cram_container
-    typedef :pointer, :cram_block
-    typedef :pointer, :cram_metrics
-
-    # cram_fd
-
-    attach_function \
-      :cram_fd_get_header,
-      [:cram_fd],
-      SamHdr.by_ref
-
-    attach_function \
-      :cram_fd_set_header,
-      [:cram_fd, SamHdr.by_ref],
-      :void
-
-    attach_function \
-      :cram_fd_get_version,
-      [:cram_fd],
-      :int
-
-    attach_function \
-      :cram_fd_set_version,
-      %i[cram_fd int],
-      :void
-
-    attach_function \
-      :cram_major_vers,
-      [:cram_fd],
-      :int
-
-    attach_function \
-      :cram_minor_vers,
-      [:cram_fd],
-      :int
-
-    attach_function \
-      :cram_fd_get_fp,
-      [:cram_fd],
-      HFile.by_ref
-
-    attach_function \
-      :cram_fd_set_fp,
-      [:cram_fd, HFile],
-      :void
-
-    attach_function \
-      :cram_container_get_length,
-      [:cram_container],
-      :int32
-
-    attach_function \
-      :cram_container_set_length,
-      %i[cram_container int32],
-      :void
-
-    attach_function \
-      :cram_container_get_num_blocks,
-      [:cram_container],
-      :int32
-
-    attach_function \
-      :cram_container_set_num_blocks,
-      %i[cram_container int32],
-      :void
-
-    attach_function \
-      :cram_container_get_landmarks,
-      %i[cram_container int32],
-      :pointer
-
-    attach_function \
-      :cram_container_set_landmarks,
-      %i[cram_container int32 pointer],
-      :void
-
-    attach_function \
-      :cram_container_get_num_records,
-      [:cram_container],
-      :int32
-
-    attach_function \
-      :cram_container_get_num_bases,
-      [:cram_container],
-      :int32
-
-    # Returns true if the container is empty (EOF marker)
-    attach_function \
-      :cram_container_is_empty,
-      [:cram_fd],
-      :int
-
-    # Returns chromosome and start/span from container struct
-    attach_function \
-      :cram_container_get_coords,
-      %i[cram_container pointer pointer],
-      :void
-
-    attach_function \
-      :cram_block_get_content_id,
-      [:cram_block],
-      :int32
-
-    attach_function \
-      :cram_block_get_comp_size,
-      [:cram_block],
-      :int32
-
-    attach_function \
-      :cram_block_get_uncomp_size,
-      [:cram_block],
-      :int32
-
-    attach_function \
-      :cram_block_get_crc32,
-      [:cram_block],
-      :int32
-
-    attach_function \
-      :cram_block_get_data,
-      [:cram_block],
-      :pointer
-
-    attach_function \
-      :cram_block_get_content_type,
-      [:cram_block],
-      CramContentType
-
-    attach_function \
-      :cram_block_get_method,
-      [:cram_block],
-      CramBlockMethod
-
-    attach_function \
-      :cram_expand_method,
-      [:pointer, :int32, CramBlockMethod],
-      :pointer
-
-    attach_function \
-      :cram_block_set_content_id,
-      %i[cram_block int32],
-      :void
-
-    attach_function \
-      :cram_block_set_comp_size,
-      %i[cram_block int32],
-      :void
-
-    attach_function \
-      :cram_block_set_uncomp_size,
-      %i[cram_block int32],
-      :void
-
-    attach_function \
-      :cram_block_set_crc32,
-      %i[cram_block int32],
-      :void
-
-    attach_function \
-      :cram_block_set_data,
-      %i[cram_block pointer],
-      :void
-
-    attach_function \
-      :cram_block_append,
-      %i[cram_block pointer int],
-      :int
-
-    attach_function \
-      :cram_block_update_size,
-      [:cram_block],
-      :void
-
-    attach_function \
-      :cram_block_get_offset,
-      [:cram_block],
-      :size_t
-
-    attach_function \
-      :cram_block_set_offset,
-      %i[cram_block size_t],
-      :void
-
-    # Computes the size of a cram block, including the block header itself.
-    attach_function \
-      :cram_block_size,
-      [:cram_block],
-      :uint32
-
-    # Returns the Block Content ID values referred to by a cram_codec in ids[2].
-    attach_function \
-      :cram_codec_get_content_ids,
-      %i[pointer pointer],
-      :void
-
-    # Produces a human readable description of the codec parameters.
-    attach_function \
-      :cram_codec_describe,
-      [:pointer, KString.ptr],
-      :int
-
-    # Renumbers RG numbers in a cram compression header.
-    attach_function \
-      :cram_transcode_rg,
-      %i[cram_fd cram_fd cram_container int pointer pointer],
-      :int
-
-    # Copies the blocks representing the next num_slice slices from a
-    # container from 'in' to 'out'.
-    attach_function \
-      :cram_copy_slice,
-      %i[cram_fd cram_fd int32],
-      :int
-
-    # Copies a container, but filtering it down to a specific region (as
-    # already specified in 'in'
-    attach_function \
-      :cram_filter_container,
-      %i[cram_fd cram_fd cram_container pointer],
-      :int
-
-    # Decodes a CRAM block compression header.
-    attach_function \
-      :cram_decode_compression_header,
-      %i[cram_fd cram_block],
-      :pointer # cram_block_compression_hdr
-
-    # Frees a cram_block_compression_hdr structure.
-    attach_function \
-      :cram_free_compression_header,
-      [:pointer],
-      :void
-
-    # Map cram block numbers to data-series.
-    attach_function \
-      :cram_update_cid2ds_map,
-      %i[pointer pointer],
-      :pointer
-
-    # Return a list of data series observed as belonging to a block with
-    # the specified content_id.
-    attach_function \
-      :cram_cid2ds_query,
-      %i[pointer int pointer],
-      :int
-
-    # Frees a cram_cid2ds_t allocated by cram_update_cid2ds_map
-    attach_function \
-      :cram_cid2ds_free,
-      [:pointer],
-      :void
-
-    # Produces a description of the record and tag encodings held within
-    # a compression header and appends to 'ks'.
-    attach_function \
-      :cram_describe_encodings,
-      [:pointer, KString.ptr],
-      :int
-
-    # Returns the number of cram blocks within this slice.
-    attach_function \
-      :cram_slice_hdr_get_num_blocks,
-      [:pointer],
-      :int32
-
-    # Returns the block content_id for the block containing an embedded
-    # reference sequence.
-    attach_function \
-      :cram_slice_hdr_get_embed_ref_id,
-      [:pointer],
-      :int
-
-    # Returns slice reference ID, start and span (length) coordinates.
-    attach_function \
-      :cram_slice_hdr_get_coords,
-      %i[pointer pointer pointer pointer],
-      :void
-
-    # Decodes a slice header from a cram block.
-    attach_function \
-      :cram_decode_slice_header,
-      %i[pointer pointer],
-      :pointer
-
-    # Frees a cram_block_slice_hdr structure.
-    attach_function \
-      :cram_free_slice_header,
-      [:pointer],
-      :void
-
-    # Allocates a new cram_block structure with a specified content_type
-    # and id.
-    attach_function \
-      :cram_new_block,
-      [CramContentType, :int],
-      :cram_block
-
-    # Reads a block from a cram file.
-    attach_function \
-      :cram_read_block,
-      [:cram_fd],
-      :cram_block
-
-    # Writes a CRAM block.
-    attach_function \
-      :cram_write_block,
-      %i[cram_fd cram_block],
-      :int
-
-    # Frees a CRAM block, deallocating internal data too.
-    attach_function \
-      :cram_free_block,
-      [:cram_block],
-      :void
-
-    # Uncompresses a CRAM block, if compressed.
-    attach_function \
-      :cram_uncompress_block,
-      [:cram_block],
-      :int
-
-    # Compresses a block.
-    attach_function \
-      :cram_compress_block,
-      %i[cram_fd cram_block cram_metrics int int],
-      :int
-
-    # Creates a new container, specifying the maximum number of slices
-    # and records permitted.
-    attach_function \
-      :cram_new_container,
-      %i[int int],
-      :cram_container
-
-    attach_function \
-      :cram_free_container,
-      [:cram_container],
-      :void
-
-    # Reads a container header.
-    attach_function \
-      :cram_read_container,
-      [:cram_fd],
-      :cram_container
-
-    # Writes a container structure.
-    attach_function \
-      :cram_write_container,
-      %i[cram_fd cram_container],
-      :int
-
-    # Stores the container structure in dat and returns *size as the
-    # number of bytes written to dat[].
-    attach_function \
-      :cram_store_container,
-      %i[cram_fd cram_container string pointer],
-      :int
-
-    attach_function \
-      :cram_container_size,
-      [:cram_container],
-      :int
-
-    # Opens a CRAM file for read (mode "rb") or write ("wb").
-    attach_function \
-      :cram_open,
-      %i[string string],
-      :cram_fd
-
-    # Opens an existing stream for reading or writing.
-    attach_function \
-      :cram_dopen,
-      %i[pointer string string],
-      :cram_fd
-
-    # Closes a CRAM file.
-    attach_function \
-      :cram_close,
-      [:cram_fd],
-      :int
-
-    # Seek within a CRAM file.
-    attach_function \
-      :cram_seek,
-      %i[pointer off_t int],
-      :int # FIXME: pointer should be :cram_fd
-
-    # Flushes a CRAM file.
-    attach_function \
-      :cram_flush,
-      [:cram_fd],
-      :int
-
-    # Checks for end of file on a cram_fd stream.
-    attach_function \
-      :cram_eof,
-      [:cram_fd],
-      :int
-
-    # Sets options on the cram_fd.
-    attach_function \
-      :cram_set_option,
-      [:cram_fd, HtsFmtOption, :varargs],
-      :int
-
-    # Sets options on the cram_fd.
-    attach_function \
-      :cram_set_voption,
-      [:cram_fd, HtsFmtOption, :pointer], # va_list
-      :int
-
-    # Attaches a header to a cram_fd.
-    attach_function \
-      :cram_set_header,
-      [:cram_fd, SamHdr.by_ref],
-      :int
-
-    # Check if this file has a proper EOF block
-    attach_function \
-      :cram_check_EOF,
-      [:cram_fd],
-      :int
-
-    # As int32_decoded/encode, but from/to blocks instead of cram_fd
-    attach_function \
-      :int32_put_blk,
-      %i[cram_block int32],
-      :int
-
-    # Returns the refs_t structure used by a cram file handle.
-    attach_function \
-      :cram_get_refs,
-      [HtsFile.by_ref],
-      :pointer # refs_t
-
-    # Returns the file offsets of CRAM slices covering a specific region query.
-    attach_function \
-      :cram_index_extents,
-      %i[cram_fd int hts_pos_t hts_pos_t pointer pointer],
-      :int
-
-    # Returns the total number of containers in the CRAM index.
-    attach_function \
-      :cram_num_containers,
-      [:cram_fd],
-      :int64
-
-    # Returns the number of containers in the CRAM index within given offsets.
-    attach_function \
-      :cram_num_containers_between,
-      %i[cram_fd off_t off_t pointer pointer],
-      :int64
-
-    # Returns the byte offset for the start of the n^th container.
-    attach_function \
-      :cram_container_num2offset,
-      %i[cram_fd int64],
-      :off_t
-
-    # Returns the container number for the first container at offset >= pos.
-    attach_function \
-      :cram_container_offset2num,
-      %i[cram_fd off_t],
-      :int64
-  end
-end

data/lib/hts/libhts/fai.rb

@@ -1,146 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    # Build index for a FASTA or FASTQ or bgzip-compressed FASTA or FASTQ file.
-    attach_function \
-      :fai_build3,
-      %i[string string string],
-      :int
-
-    # Build index for a FASTA or FASTQ or bgzip-compressed FASTA or FASTQ file.
-    attach_function \
-      :fai_build,
-      [:string],
-      :int
-
-    # Destroy a faidx_t struct
-    attach_function \
-      :fai_destroy,
-      [Faidx],
-      :void
-
-    # Load FASTA indexes.
-    attach_function \
-      :fai_load3,
-      %i[string string string int],
-      Faidx.by_ref
-
-    # Load index from "fn.fai".
-    attach_function \
-      :fai_load,
-      [:string],
-      Faidx.by_ref
-
-    #  Load FASTA or FASTQ indexes.
-    attach_function \
-      :fai_load3_format,
-      [:string, :string, :string, :int, FaiFormatOptions],
-      Faidx.by_ref
-
-    # Load index from "fn.fai".
-    attach_function \
-      :fai_load_format,
-      [:string, FaiFormatOptions],
-      Faidx.by_ref
-
-    # Fetch the sequence in a region
-    attach_function \
-      :fai_fetch,
-      [Faidx, :string, :pointer],
-      :pointer
-
-    # Fetch the sequence in a region
-    attach_function \
-      :fai_fetch64,
-      [Faidx, :string, :pointer],
-      :pointer
-
-    # Fetch the quality string for a region for FASTQ files
-    attach_function \
-      :fai_fetchqual,
-      [Faidx, :string, :pointer],
-      :pointer
-
-    attach_function \
-      :fai_fetchqual64,
-      [Faidx, :string, :pointer],
-      :pointer
-
-    # Fetch the number of sequences
-    attach_function \
-      :faidx_fetch_nseq,
-      [Faidx],
-      :int
-
-    # Fetch the sequence in a region
-    attach_function \
-      :faidx_fetch_seq,
-      [Faidx, :string, :int, :int, :pointer],
-      :pointer
-
-    # Fetch the sequence in a region
-    attach_function \
-      :faidx_fetch_seq64,
-      [Faidx, :string, :int64, :int64, :pointer],
-      :pointer
-
-    # Fetch the quality string in a region for FASTQ files
-    attach_function \
-      :faidx_fetch_qual,
-      [Faidx, :string, :int, :int, :pointer],
-      :pointer
-
-    # Fetch the quality string in a region for FASTQ files
-    attach_function \
-      :faidx_fetch_qual64,
-      [Faidx, :string, :int64, :int64, :pointer],
-      :pointer
-
-    # Query if sequence is present
-    attach_function \
-      :faidx_has_seq,
-      [Faidx, :string],
-      :int
-
-    # Return number of sequences in fai index
-    attach_function \
-      :faidx_nseq,
-      [Faidx],
-      :int
-
-    # Return name of i-th sequence
-    attach_function \
-      :faidx_iseq,
-      [Faidx, :int],
-      :string
-
-    # Return sequence length, -1 if not present
-    attach_function \
-      :faidx_seq_len,
-      [Faidx, :string],
-      :int
-
-    attach_function \
-      :faidx_seq_len64,
-      [Faidx, :string],
-      :int64
-
-    # Parses a region string.
-    attach_function \
-      :fai_parse_region,
-      [Faidx, :string, :pointer, :pointer, :pointer, :int], :string
-
-    # Sets the cache size of the underlying BGZF compressed file
-    attach_function \
-      :fai_set_cache_size,
-      [Faidx, :int],
-      :void
-
-    # Determines the path to the reference index file
-    attach_function \
-      :fai_path,
-      [:string],
-      :string
-  end
-end

data/lib/hts/libhts/hfile.rb

@@ -1,109 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    # Open the named file or URL as a stream
-    attach_function \
-      :hopen,
-      %i[string string varargs],
-      HFile.by_ref
-
-    # Associate a stream with an existing open file descriptor
-    attach_function \
-      :hdopen,
-      %i[int string],
-      HFile.by_ref
-
-    # Report whether the file name or URL denotes remote storage
-    attach_function \
-      :hisremote,
-      [:string],
-      :int
-
-    # Append an extension or replace an existing extension
-    attach_function \
-      :haddextension,
-      [KString, :string, :int, :string],
-      :string
-
-    # Flush (for output streams) and close the stream
-    attach_function \
-      :hclose,
-      [HFile],
-      :int
-
-    # Close the stream, without flushing or propagating errors
-    attach_function \
-      :hclose_abruptly,
-      [HFile],
-      :void
-
-    # Reposition the read/write stream offset
-    attach_function \
-      :hseek,
-      [HFile, :off_t, :int],
-      :off_t
-
-    # Report the current stream offset
-    def self.htell(fp)
-      base_ptr   = fp.pointer
-      begin_ptr  = base_ptr.get_pointer(fp.offset_of(:begin))
-      buffer_ptr = base_ptr.get_pointer(fp.offset_of(:buffer))
-      fp[:offset] + (begin_ptr.address - buffer_ptr.address)
-    end
-
-    # Read from the stream until the delimiter, up to a maximum length
-    attach_function \
-      :hgetdelim,
-      [:string, :size_t, :int, HFile],
-      :ssize_t
-
-    # Read a line from the stream, up to a maximum length
-    attach_function \
-      :hgets,
-      [:string, :int, HFile],
-      :string
-
-    # Peek at characters to be read without removing them from buffers
-    attach_function \
-      :hpeek,
-      [HFile, :pointer, :size_t],
-      :ssize_t
-
-    # For writing streams, flush buffered output to the underlying stream
-    attach_function \
-      :hflush,
-      [HFile],
-      :int
-
-    # For hfile_mem: get the internal buffer and it's size from a hfile
-    attach_function \
-      :hfile_mem_get_buffer,
-      [HFile, :pointer],
-      :string
-
-    # For hfile_mem: get the internal buffer and it's size from a hfile.
-    attach_function \
-      :hfile_mem_steal_buffer,
-      [HFile, :pointer],
-      :string
-
-    # Fills out sc_list[] with the list of known URL schemes.
-    attach_function \
-      :hfile_list_schemes,
-      %i[string pointer pointer], # mutable string
-      :int
-
-    # Fills out plist[] with the list of known hFILE plugins.
-    attach_function \
-      :hfile_list_plugins,
-      %i[pointer pointer], # mutable string
-      :int
-
-    # Tests for the presence of a specific hFILE plugin.
-    attach_function \
-      :hfile_has_plugin,
-      [:string],
-      :int
-  end
-end