htslib 0.0.8 → 0.2.0

data/lib/hts/libhts/constants.rb

@@ -1,8 +1,8 @@
 # frozen_string_literal: true
 
 module HTS
+  # Module for working with C HTSlib.
   module LibHTS
-    typedef :pointer, :HFILE
     typedef :int64, :hts_pos_t
     typedef :pointer, :bam_plp_auto_f
 
@@ -25,6 +25,25 @@ module HTS
         :f,              :pointer # kstream_t
     end
 
+    # HFile
+
+    class HFile < FFI::BitStruct
+      layout \
+        :buffer,        :string,
+        :begin,         :string,
+        :end,           :string,
+        :limit,         :string,
+        :backend,       :pointer,
+        :offset,        :size_t,
+        :_flags,        :uint,
+        :has_errno,     :int
+
+      bit_fields :_flags,
+                 :at_eof,     1,
+                 :mobile,     1,
+                 :readonly,   1
+    end
+
     # BGZF
     class BGZF < FFI::BitStruct
       layout \
@@ -38,7 +57,7 @@ module HTS
         :uncompressed_block,     :pointer,
         :compressed_block,       :pointer,
         :cache,                  :pointer,
-        :fp,                     :HFILE,
+        :fp,                     HFile.ptr,
         :mt,                     :pointer,
         :idx,                    :pointer,
         :idx_build_otf,          :int,
@@ -171,6 +190,16 @@ module HTS
         )
     end
 
+    class HtsReglist < FFI::Struct
+      layout \
+        :reg,            :string,
+        :intervals,      :pointer, # hts_pair_pos_t
+        :tid,            :int,
+        :count,          :uint32_t,
+        :min_beg,        :hts_pos_t,
+        :max_end,        :hts_pos_t
+    end
+
     # HtsFile
     class SamHdr < FFI::Struct
       layout \
@@ -198,8 +227,8 @@ module HTS
         :fp,
         union_layout(
           :bgzf,         BGZF.ptr,
-          :cram,         :pointer,
-          :hfile,        :pointer # HFILE
+          :cram,         :pointer, # cram_fd
+          :hfile,        HFile.ptr
         ),
         :state,          :pointer,
         :format,         HtsFormat,
@@ -245,7 +274,7 @@ module HTS
         :n_reg,          :int,
         :beg,            :int64,
         :end,            :int64,
-        :reg_list,       :pointer,
+        :reg_list,       :pointer, # HtsReglist.ptr,
         :curr_tid,       :int,
         :curr_reg,       :int,
         :curr_intv,      :int,
@@ -461,8 +490,8 @@ module HTS
         :id,             :string,
         :als,            :pointer, # (\\0-separated string)
         :allele,         :pointer,
-        :info,           :pointer, # BcfInfo.ptr,
-        :fmt,            BcfFmt.ptr,
+        :info,           :pointer, # array of BcfInfo.ptr,
+        :fmt,            :pointer, # array of BcfFmt.ptr,
         :var,            BcfVariant.ptr,
         :n_var,          :int,
         :var_type,       :int,
@@ -498,5 +527,15 @@ module HTS
         LibHTS.bcf_destroy(ptr) unless ptr.null?
       end
     end
+
+    CramContentType = enum(
+      :ct_error,           -1,
+      :file_header,        0,
+      :compression_header, 1,
+      :mapped_slice,       2,
+      :unmapped_slice,     3, # cram v1.0 only
+      :external,           4,
+      :core,               5
+    )
   end
 end

data/lib/hts/libhts/cram.rb

@@ -0,0 +1,300 @@
+# frozen_string_literal: true
+
+module HTS
+  module LibHTS
+    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

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 +29,81 @@ 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
+
+    # 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