htslib 0.0.5 → 0.0.10

data/lib/hts/libhts/cram.rb

@@ -0,0 +1,297 @@
+# frozen_string_literal: true
+
+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
+  end
+end

data/lib/hts/libhts/hfile.rb

@@ -6,13 +6,13 @@ module HTS
     attach_function \
       :hopen,
       %i[string string varargs],
-      :HFILE
+      HFILE.by_ref
 
     # Associate a stream with an existing open file descriptor
     attach_function \
       :hdopen,
       %i[int string],
-      :HFILE
+      HFILE.by_ref
 
     # Report whether the file name or URL denotes remote storage
     attach_function \
@@ -29,55 +29,63 @@ 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,
-      %i[HFILE off_t int],
+      [HFILE, :off_t, :int],
       :off_t
 
+    # Report the current stream offset
+    def self.htell(fp)
+      # TODO: This is a hack. Is this OK?
+      bg = FFI::Pointer.new(:int, fp.pointer.address + fp.offset_of(:begin)).read_int
+      bf = FFI::Pointer.new(:int, fp.pointer.address + fp.offset_of(:buffer)).read_int
+      fp[:offset] + (bg - bf)
+    end
+
     # Read from the stream until the delimiter, up to a maximum length
     attach_function \
       :hgetdelim,
-      %i[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,
-      %i[string int HFILE],
+      [:string, :int, HFILE],
       :string
 
     # Peek at characters to be read without removing them from buffers
     attach_function \
       :hpeek,
-      %i[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,
-      %i[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,
-      %i[HFILE pointer],
+      [HFILE, :pointer],
       :string
   end
 end

data/lib/hts/libhts/hts.rb

@@ -61,7 +61,7 @@ module HTS
     # Determine format by peeking at the start of a file
     attach_function \
       :hts_detect_format,
-      [:HFILE, HtsFormat],
+      [HFILE, HtsFormat],
       :int
 
     # Get a human-readable description of the file format
@@ -86,9 +86,15 @@ module HTS
     # Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file
     attach_function \
       :hts_hopen,
-      %i[HFILE string string],
+      [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,
@@ -139,7 +145,7 @@ module HTS
     # Create extra threads to aid compress/decompression for this file
     attach_function \
       :hts_set_thread_pool,
-      [HtsFile, HtsThreadPool],
+      [HtsFile, HtsTpool],
       :int
 
     # Adds a cache of decompressed blocks, potentially speeding up seeks.