htslib 0.0.10 → 0.2.1

data/lib/hts/libhts/cram.rb

@@ -2,296 +2,299 @@
 
 module HTS
   module LibHTS
-
-=begin
-
-attach_function \
-  :cram_fd_get_header,
-  [CramFd],
-  SamHdr.by_ref
-
-attach_function \
-  :cram_fd_set_header,
-  [CramFd, SamHdr.by_ref],
-  :void
-  
-attach_function \
-  :cram_fd_get_version,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_fd_set_version,
-  [CramFd, :int],
-  :void
-
-attach_function \
-  :cram_major_vers,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_minor_vers,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_fd_get_fp,
-  [CramFd],
-  HFile.by_ref
-
-attach_function \
-  :cram_fd_set_fp,
-  [CramFd, HFile],
-  :void
-
-attach_function \
-  :cram_container_get_length,
-  [CramContainer],
-  :int32
-
-attach_function \
-  :cram_container_set_length,
-  [CramContainer, :int32],
-  :void
-
-attach_function \
-  :cram_container_get_num_blocks,
-  [CramContainer],
-  :int32
-
-attach_function \
-  :cram_container_set_num_blocks,
-  [CramContainer, :int32],
-  :void
-  
-attach_function \
-  :cram_container_get_landmarks,
-  [CramContainer, :int32],
-  :pointer
-
-attach_function \
-  :cram_container_set_landmarks,
-  [CramContainer, :Int32, :pointer],
-  :void
-
-attach_function \
-  :cram_container_is_empty,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_block_get_content_id,
-  [CramBlock],
-  :int32
-
-attach_function \
-  :cram_block_get_comp_size,
-  [CramBlock],
-  :int32
-
-attach_function \
-  :cram_block_get_uncomp_size,
-  [CramBlock],
-  :int32
-
-attach_function \
-  :cram_block_get_crc32,
-  [CramBlock],
-  :int32
-
-attach_function \
-  :cram_block_get_data,
-  [CramBlock],
-  :pointer
-
-attach_function \
-  :cram_block_get_content_type,
-  [CramBlock],
-  CramContentType                # ?
-
-attach_function \
-  :cram_block_set_content_id,
-  [CramBlock, :int32],
-  :void
-  
-attach_function \
-  :cram_block_set_comp_size,
-  [CramBlock, :int32],
-  :void
-
-attach_function \
-  :cram_block_set_uncomp_size,
-  [CramBlock, :int32],
-  :void
-  
-attach_function \
-  :cram_block_set_crc32,
-  [CramBlock, :int32],
-  :void
-
-attach_function \
-  :cram_block_set_data,
-  [CramBlock, :pointer],
-  :void
-
-attach_function \
-  :cram_block_append,
-  [CramBlock, :pointer, :int],
-  :int
-
-attach_function \
-  :cram_block_update_size,
-  [CramBlock],
-  :void
-
-attach_function \
-  :cram_block_get_offset,
-  [CramBlock],
-  :size_t
-
-attach_function \
-  :cram_block_set_offset,
-  [CramBlock, :size_t],
-  :void
-
-attach_function \
-  :cram_block_size,
-  [CramBlock],
-  :uint32
-
-attach_function \
-  :cram_transcode_rg,
-  [CramFd, CramFd, CramContainer, :int, :pointer, :pointer],
-  :int
-
-attach_function \
-  :cram_copy_slice,
-  [CramFd, CramFd, :int32],
-  :int
-
-attach_function \
-  :cram_new_block,
-  [CramContentType, :int],
-  CramBlock
-
-attach_function \
-  :cram_read_block,
-  [CramFd],
-  CramBlock
-
-attach_function \
-  :cram_write_block,
-  [CramFd, CramBlock],
-  :int
-
-attach_function \
-  :cram_free_block,
-  [CramBlock],
-  :void
-  
-attach_function \
-  :cram_uncompress_block,
-  [CramBlock],
-  :int
-
-attach_function \
-  :cram_compress_block,
-  [CramFd, CramBlock, CramMetrics, :int, :int],
-  :int
-
-attach_function \
-  :cram_compress_block2,
-  [CramFd, CramSlice, CramBlock, CramMetrics, :int, :int],
-  :int
-
-attach_function \
-  :cram_new_container,
-  [:int, :int],
-  CramContainer
-
-attach_function \
-  :cram_free_container,
-  [CramContainer],
-  :void
-
-attach_function \
-  :cram_read_container,
-  [CramFd],
-  CramContainer
-
-attach_function \
-  :cram_write_container,
-  [CramFd, CramContainer],
-  :int
-
-attach_function \
-  :cram_store_container,
-  [CramFd, CramContainer, :string, :pointer],
-  :int
-
-attach_function \
-  :cram_container_size,
-  [CramContainer],
-  :int
-
-attach_function \
-  :cram_open,
-  [:string, :string],
-  CramFd
-
-attach_function \
-  :cram_dopen,
-  [:pointer, :string, :string],
-  CramFd
-
-attach_function \
-  :cram_close,
-  [CramFd],
-  :int
-
-=end
-
-attach_function \
-  :cram_seek,
-  [:pointer, :off_t, :int], :int # FIXME pointer should be CramFd
-
-=begin
-
-attach_function \
-  :cram_flush,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_eof,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_set_option,
-  [CramFd, HtsFmtOption, ...], # vararg!
-  :int
-
-attach_function \
-  :cram_set_voption,
-  [CramFd, HtsFmtOption, VaList],
-  :int
-
-attach_function \
-  :cram_set_header,
-  [CramFd, SamHdr.by_ref],
-  :int
-
-attach_function \
-  :cram_check_eof = :cram_check_EOF,
-  [CramFd], :int
-
-attach_function \
-  :cram_get_refs,
-  [HtsFile],
-  RefsT # what is RefsT
-
-=end
+    typedef :pointer, :cram_fd
+    typedef :pointer, :cram_container
+    typedef :pointer, :cram_block
+    typedef :pointer, :cram_metrics
+
+    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_is_empty,
+      [:cram_fd],
+      :int
+
+    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_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
+
+    attach_function \
+      :cram_block_size,
+      [:cram_block],
+      :uint32
+
+    attach_function \
+      :cram_transcode_rg,
+      %i[cram_fd cram_fd cram_container int pointer pointer],
+      :int
+
+    attach_function \
+      :cram_copy_slice,
+      %i[cram_fd cram_fd int32],
+      :int
+
+    attach_function \
+      :cram_new_block,
+      [CramContentType, :int],
+      :cram_block
+
+    attach_function \
+      :cram_read_block,
+      [:cram_fd],
+      :cram_block
+
+    attach_function \
+      :cram_write_block,
+      %i[cram_fd cram_block],
+      :int
+
+    attach_function \
+      :cram_free_block,
+      [:cram_block],
+      :void
+
+    attach_function \
+      :cram_uncompress_block,
+      [:cram_block],
+      :int
+
+    attach_function \
+      :cram_compress_block,
+      %i[cram_fd cram_block cram_metrics int int],
+      :int
+
+    # attach_function \
+    #   :cram_compress_block2,
+    #   %i[cram_fd cram_slice cram_block cram_metrics int int],
+    #   :int
+
+    attach_function \
+      :cram_new_container,
+      %i[int int],
+      :cram_container
+
+    attach_function \
+      :cram_free_container,
+      [:cram_container],
+      :void
+
+    attach_function \
+      :cram_read_container,
+      [:cram_fd],
+      :cram_container
+
+    attach_function \
+      :cram_write_container,
+      %i[cram_fd cram_container],
+      :int
+
+    attach_function \
+      :cram_store_container,
+      %i[cram_fd cram_container string pointer],
+      :int
+
+    attach_function \
+      :cram_container_size,
+      [:cram_container],
+      :int
+
+    attach_function \
+      :cram_open,
+      %i[string string],
+      :cram_fd
+
+    attach_function \
+      :cram_dopen,
+      %i[pointer string string],
+      :cram_fd
+
+    attach_function \
+      :cram_close,
+      [:cram_fd],
+      :int
+
+    attach_function \
+      :cram_seek,
+      %i[pointer off_t int],
+      :int # FIXME: pointer should be :cram_fd
+
+    attach_function \
+      :cram_flush,
+      [:cram_fd],
+      :int
+
+    attach_function \
+      :cram_eof,
+      [:cram_fd],
+      :int
+
+    attach_function \
+      :cram_set_option,
+      [:cram_fd, HtsFmtOption, :varargs],
+      :int
+
+    attach_function \
+      :cram_set_voption,
+      [:cram_fd, HtsFmtOption, :pointer], # va_list
+      :int
+
+    attach_function \
+      :cram_set_header,
+      [:cram_fd, SamHdr.by_ref],
+      :int
+
+    attach_function \
+      :cram_check_EOF,
+      [:cram_fd],
+      :int
+
+    attach_function \
+      :int32_put_blk,
+      %i[cram_block int32_t],
+      :int
+
+    attach_function \
+      :cram_get_refs,
+      [HtsFile.by_ref],
+      :pointer # refs_t
   end
-end
+end

data/lib/hts/libhts/hfile.rb

@@ -6,13 +6,13 @@ module HTS
     attach_function \
       :hopen,
       %i[string string varargs],
-      HFILE.by_ref
+      HFile.by_ref
 
     # Associate a stream with an existing open file descriptor
     attach_function \
       :hdopen,
       %i[int string],
-      HFILE.by_ref
+      HFile.by_ref
 
     # Report whether the file name or URL denotes remote storage
     attach_function \
@@ -29,19 +29,19 @@ module HTS
     # Flush (for output streams) and close the stream
     attach_function \
       :hclose,
-      [HFILE],
+      [HFile],
       :int
 
     # Close the stream, without flushing or propagating errors
     attach_function \
       :hclose_abruptly,
-      [HFILE],
+      [HFile],
       :void
 
     # Reposition the read/write stream offset
     attach_function \
       :hseek,
-      [HFILE, :off_t, :int],
+      [HFile, :off_t, :int],
       :off_t
 
     # Report the current stream offset
@@ -55,37 +55,55 @@ module HTS
     # Read from the stream until the delimiter, up to a maximum length
     attach_function \
       :hgetdelim,
-      [:string, :size_t, :int, HFILE],
+      [: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, :int, HFile],
       :string
 
     # Peek at characters to be read without removing them from buffers
     attach_function \
       :hpeek,
-      [HFILE, :pointer, :size_t],
+      [HFile, :pointer, :size_t],
       :ssize_t
 
     # For writing streams, flush buffered output to the underlying stream
     attach_function \
       :hflush,
-      [HFILE],
+      [HFile],
       :int
 
     # For hfile_mem: get the internal buffer and it's size from a hfile
     attach_function \
       :hfile_mem_get_buffer,
-      [HFILE, :pointer],
+      [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],
+      [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