htslib 0.4.1 → 0.5.0

data/lib/hts/libhts/hts.rb

@@ -1,477 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    # hts_expand
-    # hts_expand3
-    # hts_resize
-
-    # Sets the selected log level.
-    attach_function \
-      :hts_set_log_level,
-      [HtsLogLevel],
-      :void
-
-    # Gets the selected log level.
-    attach_function \
-      :hts_get_log_level,
-      [],
-      HtsLogLevel
-
-    attach_function \
-      :hts_lib_shutdown,
-      [],
-      :void
-
-    attach_function \
-      :hts_free,
-      [:pointer],
-      :void
-
-    # Parses arg and appends it to the option list.
-    attach_function \
-      :hts_opt_add,
-      %i[pointer string],
-      :int
-
-    # Applies an hts_opt option list to a given htsFile.
-    attach_function \
-      :hts_opt_apply,
-      [HtsFile, HtsOpt],
-      :int
-
-    # Frees an hts_opt list.
-    attach_function \
-      :hts_opt_free,
-      [HtsOpt],
-      :void
-
-    # Accepts a string file format (sam, bam, cram, vcf, bam)
-    attach_function \
-      :hts_parse_format,
-      [HtsFormat, :string],
-      :int
-
-    # Tokenise options as (key(=value)?,)*(key(=value)?)?
-    attach_function \
-      :hts_parse_opt_list,
-      [HtsFormat, :string],
-      :int
-
-    # Get the htslib version number
-    attach_function \
-      :hts_version,
-      [],
-      :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],
-      :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
-    attach_function \
-      :hts_format_description,
-      [HtsFormat],
-      :string
-
-    # Open a sequence data (SAM/BAM/CRAM) or variant data (VCF/BCF)
-    # or possibly-compressed textual line-orientated file
-    attach_function \
-      :hts_open,
-      %i[string string],
-      HtsFile.by_ref
-
-    # Open a SAM/BAM/CRAM/VCF/BCF/etc file
-    attach_function \
-      :hts_open_format,
-      [:string, :string, HtsFormat],
-      HtsFile.by_ref
-
-    # Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file
-    attach_function \
-      :hts_hopen,
-      [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,
-      [HtsFile],
-      :int
-
-    # Returns the file's format information
-    attach_function \
-      :hts_get_format,
-      [HtsFile],
-      HtsFormat.by_ref
-
-    # Returns a string containing the file format extension.
-    attach_function \
-      :hts_format_file_extension,
-      [HtsFormat],
-      :string
-
-    # Sets a specified CRAM option on the open file handle.
-    attach_function \
-      :hts_set_opt,
-      [HtsFile, HtsFmtOption, :varargs],
-      :int
-
-    # Read a line (and its \n or \r\n terminator) from a file
-    attach_function \
-      :hts_getline,
-      [HtsFile, :int, KString],
-      :int
-
-    attach_function \
-      :hts_readlines,
-      %i[string pointer],
-      :pointer
-
-    # Parse comma-separated list or read list from a file
-    attach_function \
-      :hts_readlist,
-      %i[string int pointer],
-      :pointer
-
-    # Create extra threads to aid compress/decompression for this file
-    attach_function \
-      :hts_set_threads,
-      [HtsFile, :int],
-      :int
-
-    # Create extra threads to aid compress/decompression for this file
-    attach_function \
-      :hts_set_thread_pool,
-      [HtsFile, HtsTpool],
-      :int
-
-    # Adds a cache of decompressed blocks, potentially speeding up seeks.
-    attach_function \
-      :hts_set_cache_size,
-      [HtsFile, :int],
-      :void
-
-    # Set .fai filename for a file opened for reading
-    attach_function \
-      :hts_set_fai_filename,
-      [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,
-      [HtsFile],
-      :int
-
-    # hts_pair_pos_t
-    # hts_pair64_t
-    # hts_pair4_max_t
-    # hts_reglist_t
-    # hts_readrec_func
-    # hts_seek_func
-    # hts_tell_func
-
-    # Create a BAI/CSI/TBI type index structure
-    attach_function \
-      :hts_idx_init,
-      %i[int int uint64 int int],
-      :pointer
-
-    # Free a BAI/CSI/TBI type index
-    attach_function \
-      :hts_idx_destroy,
-      [HtsIdx],
-      :void
-
-    # Push an index entry
-    attach_function \
-      :hts_idx_push,
-      [HtsIdx, :int, :int64, :int64, :uint64, :int],
-      :int
-
-    # Finish building an index
-    attach_function \
-      :hts_idx_finish,
-      [HtsIdx, :uint64],
-      :int
-
-    # Returns index format
-    attach_function \
-      :hts_idx_fmt,
-      [HtsIdx],
-      :int
-
-    # Add name to TBI index meta-data
-    attach_function \
-      :hts_idx_tbi_name,
-      [HtsIdx, :int, :string],
-      :int
-
-    # Save an index to a file
-    attach_function \
-      :hts_idx_save,
-      [HtsIdx, :string, :int],
-      :int
-
-    # Save an index to a specific file
-    attach_function \
-      :hts_idx_save_as,
-      [HtsIdx, :string, :string, :int],
-      :int
-
-    # Load an index file
-    attach_function \
-      :hts_idx_load,
-      %i[string int],
-      HtsIdx.by_ref
-
-    # Load a specific index file
-    attach_function \
-      :hts_idx_load2,
-      %i[string string],
-      HtsIdx.by_ref
-
-    # Load a specific index file
-    attach_function \
-      :hts_idx_load3,
-      %i[string string int int],
-      HtsIdx.by_ref
-
-    # Get extra index meta-data
-    attach_function \
-      :hts_idx_get_meta,
-      [HtsIdx, :pointer],
-      :uint8
-
-    # Set extra index meta-data
-    attach_function \
-      :hts_idx_set_meta,
-      [HtsIdx, :uint32, :pointer, :int],
-      :int
-
-    # Get number of mapped and unmapped reads from an index
-    attach_function \
-      :hts_idx_get_stat,
-      [HtsIdx, :int, :pointer, :pointer],
-      :int
-
-    # Return the number of unplaced reads from an index
-    attach_function \
-      :hts_idx_get_n_no_coor,
-      [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,
-      %i[string pointer pointer],
-      :string
-
-    # Parse a "CHR:START-END"-style region string
-    attach_function \
-      :hts_parse_reg,
-      %i[string pointer pointer],
-      :string
-
-    # Parse a "CHR:START-END"-style region string
-    attach_function \
-      :hts_parse_region,
-      %i[string pointer pointer pointer hts_name2id_f pointer int],
-      :string
-
-    # Create a single-region iterator
-    attach_function \
-      :hts_itr_query,
-      [HtsIdx, :int, :hts_pos_t, :hts_pos_t, :pointer],
-      HtsItr.by_ref
-
-    # Free an iterator
-    attach_function \
-      :hts_itr_destroy,
-      [HtsItr],
-      :void
-
-    # Create a single-region iterator from a text region specification
-    attach_function \
-      :hts_itr_querys,
-      [HtsIdx, :string, :hts_name2id_f, :pointer, :pointer, :pointer],
-      HtsItr.by_ref
-
-    # Return the next record from an iterator
-    attach_function \
-      :hts_itr_next,
-      [BGZF, HtsItr, :pointer, :pointer],
-      :int
-
-    attach_function \
-      :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
-
-    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], # unsigned 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
-
-    # Computes CRC32 for a buffer with an initial crc value
-    attach_function \
-      :hts_crc32,
-      %i[uint32 pointer size_t],
-      :uint32
-  end
-end

data/lib/hts/libhts/kfunc.rb

@@ -1,38 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    # Log gamma function
-    attach_function \
-      :kf_lgamma,
-      [:double],
-      :double
-
-    # complementary error function
-    attach_function \
-      :kf_erfc,
-      [:double],
-      :double
-
-    # The following computes regularized incomplete gamma functions.
-    attach_function \
-      :kf_gammap,
-      %i[double double],
-      :double
-
-    attach_function \
-      :kf_gammaq,
-      %i[double double],
-      :double
-
-    attach_function \
-      :kf_betai,
-      %i[double double double],
-      :double
-
-    attach_function \
-      :kt_fisher_exact,
-      %i[int int int int pointer pointer pointer],
-      :double
-  end
-end