htslib 0.1.0 → 0.2.2

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

data/lib/hts/libhts/hts.rb

@@ -6,7 +6,13 @@ module HTS
     # hts_expand3
     # hts_resize
 
-    # hts_log.h
+    # Sets the selected log level.
+    attach_function \
+      :hts_set_log_level,
+      [HtsLogLevel],
+      :void
+
+    # Gets the selected log level.
     attach_function \
       :hts_get_log_level,
       [],
@@ -58,10 +64,33 @@ module HTS
       [],
       :string
 
+    # Introspection on the features enabled in htslib
+    attach_function \
+      :hts_features,
+      [],
+      :uint
+
+    attach_function \
+      :hts_test_feature,
+      [:uint],
+      :string
+
+    # Introspection on the features enabled in htslib, string form
+    attach_function \
+      :hts_feature_string,
+      [],
+      :string
+
     # Determine format by peeking at the start of a file
     attach_function \
       :hts_detect_format,
-      [HFILE, HtsFormat],
+      [HFile, HtsFormat],
+      :int
+
+    # Determine format primarily by peeking at the start of a file
+    attach_function \
+      :hts_detect_format2,
+      [HFile, :string, HtsFormat],
       :int
 
     # Get a human-readable description of the file format
@@ -86,7 +115,7 @@ module HTS
     # Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file
     attach_function \
       :hts_hopen,
-      [HFILE, :string, :string],
+      [HFile, :string, :string],
       HtsFile.by_ref
 
     # For output streams, flush any buffered data
@@ -160,6 +189,12 @@ module HTS
       [HtsFile, :string],
       :int
 
+    # Sets a filter expression
+    attach_function \
+      :hts_set_filter_expression,
+      [HtsFile, :string],
+      :int
+
     # Determine whether a given htsFile contains a valid EOF block
     attach_function \
       :hts_check_EOF,
@@ -264,11 +299,26 @@ module HTS
       [HtsIdx],
       :uint64
 
+    # Return a list of target names from an index
+    attach_function \
+      :hts_idx_seqnames,
+      [HtsIdx, :pointer, :pointer, :pointer],
+      :pointer
+
+    #  Return the number of targets from an index
+    attach_function \
+      :hts_idx_nseq,
+      [HtsIdx],
+      :int
+
+    # Parse a numeric string
     attach_function \
       :hts_parse_decimal,
       %i[string pointer int],
       :long_long
 
+    callback :hts_name2id_f, %i[pointer string], :int
+
     # Parse a "CHR:START-END"-style region string
     attach_function \
       :hts_parse_reg64,
@@ -284,7 +334,7 @@ module HTS
     # Parse a "CHR:START-END"-style region string
     attach_function \
       :hts_parse_region,
-      %i[string pointer pointer pointer pointer pointer int],
+      %i[string pointer pointer pointer hts_name2id_f pointer int],
       :string
 
     # Create a single-region iterator
@@ -302,7 +352,7 @@ module HTS
     # Create a single-region iterator from a text region specification
     attach_function \
       :hts_itr_querys,
-      [HtsIdx, :string, :pointer, :pointer, :pointer, :pointer],
+      [HtsIdx, :string, :hts_name2id_f, :pointer, :pointer, :pointer],
       HtsItr.by_ref
 
     # Return the next record from an iterator
@@ -312,27 +362,110 @@ module HTS
       :int
 
     attach_function \
-      :hts_idx_seqnames,
-      [HtsIdx, :pointer, :pointer, :pointer],
+      :hts_itr_multi_bam,
+      [HtsIdx, HtsItr],
+      :int
+
+    attach_function \
+      :hts_itr_multi_cram,
+      [HtsIdx, HtsItr],
+      :int
+
+    # Create a multi-region iterator from a region list
+    attach_function \
+      :hts_itr_regions,
+      [HtsIdx,
+       :pointer, # hts_reglist_t *
+       :int,
+       :hts_name2id_f,
+       :pointer,
+       :pointer, # hts_itr_multi_query_func
+       :pointer, # hts_readrec_func
+       :pointer, # hts_seek_func
+       :pointer  # hts_tell_func
+      ],
+      HtsItr.by_ref
+
+    # Return the next record from an iterator
+    attach_function \
+      :hts_itr_multi_next,
+      [HtsFile, HtsItr, :pointer],
+      :int
+
+    # Create a region list from a char array
+    attach_function \
+      :hts_reglist_create,
+      %i[pointer int pointer pointer hts_name2id_f],
+      HtsReglist.by_ref
+
+    # Free a region list
+    attach_function \
+      :hts_reglist_free,
+      [HtsReglist, :int],
+      :void
+
+    # Deprecated
+    # Convenience function to determine file type
+    # attach_function \
+    #   :hts_file_type,
+    #   [:string],
+    #   :int
+
+    attach_function \
+      :errmod_init,
+      [:double],
       :pointer
 
-    # hts_itr_multi_bam
-    # hts_itr_multi_cram
-    # hts_itr_regions
-    # hts_itr_multi_next
-    # hts_reglist_create
-    # hts_reglist_free
-    # errmod_init
-    # errmod_destroy
-    # errmod_call
-    # proabln_glocal
-    # hts_md5_context
-    # hts_md5_update
-    # hts_md5_final
-    # hts_md5_reset
-    # hts_md5_hex
-    # hts_md5_destroy
-
-    # attach_function :sam_hdr_tid2name,          [:pointer, :int],                             :string
+    attach_function \
+      :errmod_destroy,
+      [:pointer],
+      :void
+
+    attach_function \
+      :errmod_cal,
+      %i[pointer int int pointer pointer],
+      :int
+
+    # Perform probabilistic banded glocal alignment
+    attach_function \
+      :probaln_glocal,
+      %i[pointer int pointer int pointer pointer pointer pointer],
+      :int
+
+    # Initialises an MD5 context.
+    attach_function \
+      :hts_md5_init,
+      [],
+      :pointer # hts_md5_context
+
+    # Updates the context with the MD5 of the data.
+    attach_function \
+      :hts_md5_update,
+      %i[pointer pointer ulong],
+      :void
+
+    # Computes the final 128-bit MD5 hash from the given context
+    attach_function \
+      :hts_md5_final,
+      %i[pointer pointer], # unsinged char
+      :void
+
+    #  Resets an md5_context to the initial state, as returned by hts_md5_init().
+    attach_function \
+      :hts_md5_reset,
+      [:pointer],
+      :void
+
+    # Converts a 128-bit MD5 hash into a 33-byte nul-termninated by string.
+    attach_function \
+      :hts_md5_hex,
+      %i[string pointer],
+      :void
+
+    #  Deallocates any memory allocated by hts_md5_init.
+    attach_function \
+      :hts_md5_destroy,
+      [:pointer],
+      :void
   end
 end