htslib 0.4.2 → 0.5.0

data/lib/hts/libhts/vcf.rb

@@ -1,567 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    # Get error description for bcf error code
-    attach_function \
-      :bcf_strerror,
-      %i[int pointer size_t],
-      :string
-
-    # Create an empty BCF header.
-    attach_function \
-      :bcf_hdr_init,
-      [:string],
-      BcfHdr.by_ref
-
-    # Destroy a BCF header struct
-    attach_function \
-      :bcf_hdr_destroy,
-      [BcfHdr],
-      :void
-
-    # Allocate and initialize a bcf1_t object.
-    attach_function \
-      :bcf_init,
-      [],
-      Bcf1.by_ref
-
-    # Deallocate a bcf1_t object
-    attach_function \
-      :bcf_destroy,
-      [Bcf1],
-      :void
-
-    # Same as bcf_destroy() but frees only the memory allocated by bcf1_t,
-    # not the bcf1_t object itself.
-    attach_function \
-      :bcf_empty,
-      [Bcf1],
-      :void
-
-    # Make the bcf1_t object ready for next read.
-    attach_function \
-      :bcf_clear,
-      [Bcf1],
-      :void
-
-    # Read a VCF or BCF header
-    attach_function \
-      :bcf_hdr_read,
-      [HtsFile],
-      BcfHdr.by_ref
-
-    # for more efficient VCF parsing when only one/few samples are needed
-    attach_function \
-      :bcf_hdr_set_samples,
-      [BcfHdr, :string, :int],
-      :int
-
-    attach_function \
-      :bcf_subset_format,
-      [BcfHdr, Bcf1],
-      :int
-
-    # Write a VCF or BCF header
-    attach_function \
-      :bcf_hdr_write,
-      [HtsFile, BcfHdr],
-      :int
-
-    # Parse VCF line contained in kstring and populate the bcf1_t struct
-    attach_function \
-      :vcf_parse,
-      [KString, BcfHdr, Bcf1],
-      :int
-
-    # Complete the file opening mode, according to its extension.
-    attach_function \
-      :vcf_open_mode,
-      %i[string string string],
-      :int
-
-    # The opposite of vcf_parse.
-    attach_function \
-      :vcf_format,
-      [BcfHdr, Bcf1, KString],
-      :int
-
-    # Read next VCF or BCF record
-    attach_function \
-      :bcf_read,
-      [HtsFile, BcfHdr, Bcf1],
-      :int
-
-    # unpack/decode a BCF record (fills the bcf1_t::d field)
-    attach_function \
-      :bcf_unpack,
-      [Bcf1, :int],
-      :int
-
-    # Create a copy of BCF record.
-    attach_function \
-      :bcf_dup,
-      [Bcf1],
-      Bcf1.by_ref
-
-    attach_function \
-      :bcf_copy,
-      [Bcf1, Bcf1],
-      Bcf1.by_ref
-
-    # Write one VCF or BCF record.
-    attach_function \
-      :bcf_write,
-      [HtsFile, BcfHdr, Bcf1],
-      :int
-
-    # Read a VCF format header
-    attach_function \
-      :vcf_hdr_read,
-      [HtsFile],
-      BcfHdr.by_ref
-
-    # Write a VCF format header
-    attach_function \
-      :vcf_hdr_write,
-      [HtsFile, BcfHdr],
-      :int
-
-    # Read a record from a VCF file
-    attach_function \
-      :vcf_read,
-      [HtsFile, BcfHdr, Bcf1],
-      :int
-
-    # Write a record to a VCF file
-    attach_function \
-      :vcf_write,
-      [HtsFile, BcfHdr, Bcf1],
-      :int
-
-    # Helper function for the bcf_itr_next() macro
-    attach_function \
-      :bcf_readrec,
-      [BGZF, :pointer, :pointer, :pointer, :hts_pos_t, :hts_pos_t],
-      :int
-
-    attach_function \
-      :bcf_itr_querys1,
-      [HtsIdx, BcfHdr, :string],
-      HtsItr.by_ref
-
-    attach_function \
-      :bcf_itr_regarray,
-      [HtsIdx, BcfHdr, :pointer, :uint],
-      HtsItr.by_ref
-
-    # Write a line to a VCF file
-    attach_function \
-      :vcf_write_line,
-      [HtsFile, KString],
-      :int
-
-    # Header querying and manipulation routines
-
-    # Create a new header using the supplied template
-    attach_function \
-      :bcf_hdr_dup,
-      [BcfHdr],
-      BcfHdr.by_ref
-
-    # DEPRECATED please use bcf_hdr_merge instead
-    #
-    # attach_function \
-    #   :bcf_hdr_combine,
-    #   [BcfHdr, BcfHdr],
-    #   :int
-
-    # Copy header lines from src to dst, see also bcf_translate()
-    attach_function \
-      :bcf_hdr_merge,
-      [BcfHdr, BcfHdr],
-      BcfHdr.by_ref
-
-    # Add a new sample.
-    attach_function \
-      :bcf_hdr_add_sample,
-      [BcfHdr, :string],
-      :int
-
-    # Read VCF header from a file and update the header
-    attach_function \
-      :bcf_hdr_set,
-      [BcfHdr, :string],
-      :int
-
-    # Appends formatted header text to _str_.
-    attach_function \
-      :bcf_hdr_format,
-      [BcfHdr, :int, KString],
-      :int
-
-    # DEPRECATED use bcf_hdr_format() instead
-    #
-    # attach_function \
-    #   :bcf_hdr_fmt_text,
-    #   [BcfHdr, :int, :pointer],
-    #   :string
-
-    # Append new VCF header line
-    attach_function \
-      :bcf_hdr_append,
-      [BcfHdr, :string],
-      :int
-
-    attach_function \
-      :bcf_hdr_printf,
-      [BcfHdr, :string, :varargs],
-      :int
-
-    # VCF version, e.g. VCFv4.2
-    attach_function \
-      :bcf_hdr_get_version,
-      [BcfHdr],
-      :string
-
-    # Set version in bcf header
-    attach_function \
-      :bcf_hdr_set_version,
-      [BcfHdr, :string],
-      :int
-
-    # Remove VCF header tag
-    attach_function \
-      :bcf_hdr_remove,
-      [BcfHdr, :int, :string],
-      :void
-
-    # Creates a new copy of the header removing unwanted samples
-    attach_function \
-      :bcf_hdr_subset,
-      [BcfHdr, :int, :pointer, :pointer],
-      BcfHdr.by_ref
-
-    # Creates a list of sequence names.
-    attach_function \
-      :bcf_hdr_seqnames,
-      [BcfHdr, :pointer],
-      :pointer
-
-    attach_function \
-      :bcf_hdr_parse,
-      [BcfHdr, :string],
-      :int
-
-    # Synchronize internal header structures
-    attach_function \
-      :bcf_hdr_sync,
-      [BcfHdr],
-      :int
-
-    # parse a single line of VCF textual header
-    attach_function \
-      :bcf_hdr_parse_line,
-      [BcfHdr, :string, :pointer],
-      BcfHrec.by_ref
-
-    # Convert a bcf header record to string form
-    attach_function \
-      :bcf_hrec_format,
-      [BcfHrec, KString],
-      :int
-
-    attach_function \
-      :bcf_hdr_add_hrec,
-      [BcfHdr, BcfHrec],
-      :int
-
-    # Get header line info
-    attach_function \
-      :bcf_hdr_get_hrec,
-      [BcfHdr, :int, :string, :string, :string],
-      :pointer
-
-    # Duplicate a header record
-    attach_function \
-      :bcf_hrec_dup,
-      [:pointer],
-      BcfHrec.by_ref
-
-    # Add a new header record key
-    attach_function \
-      :bcf_hrec_add_key,
-      [BcfHrec, :string, :size_t],
-      :int
-
-    # Set a header record value
-    attach_function \
-      :bcf_hrec_set_val,
-      [BcfHrec, :int, :string, :size_t, :int],
-      :int
-
-    attach_function \
-      :bcf_hrec_find_key,
-      [BcfHrec, :string],
-      :int
-
-    # Add an IDX header record
-    attach_function \
-      :hrec_add_idx,
-      [BcfHrec, :int],
-      :int
-
-    # Free up a header record and associated structures
-    attach_function \
-      :bcf_hrec_destroy,
-      [:pointer],
-      :void
-
-    # Individual record querying and manipulation routines
-
-    # See the description of bcf_hdr_subset()
-    attach_function \
-      :bcf_subset,
-      [BcfHdr, Bcf1, :int, :pointer],
-      :int
-
-    # Translate tags ids to be consistent with different header.
-    attach_function \
-      :bcf_translate,
-      [BcfHdr, BcfHdr, Bcf1],
-      :int
-
-    # Get variant types in a BCF record
-    attach_function \
-      :bcf_get_variant_types,
-      [Bcf1],
-      :int
-
-    # Get variant type in a BCF record, for a given allele
-    attach_function \
-      :bcf_get_variant_type,
-      [Bcf1, :int],
-      :int
-
-    # Check for presence of variant types in a BCF record
-    attach_function \
-      :bcf_has_variant_types,
-      [Bcf1, :uint32, :int],
-      :int
-
-    # Check for presence of variant types in a BCF record, for a given allele
-    attach_function \
-      :bcf_has_variant_type,
-      [Bcf1, :int, :uint32],
-      :int
-
-    # Return the number of bases affected by a variant, for a given allele
-    attach_function \
-      :bcf_variant_length,
-      [Bcf1, :int],
-      :int
-
-    attach_function \
-      :bcf_is_snp,
-      [Bcf1],
-      :int
-
-    # Sets the FILTER column
-    attach_function \
-      :bcf_update_filter,
-      [BcfHdr, Bcf1, :pointer, :int],
-      :int
-
-    # Adds to the FILTER column
-    attach_function \
-      :bcf_add_filter,
-      [BcfHdr, Bcf1, :int],
-      :int
-
-    # Removes from the FILTER column
-    attach_function \
-      :bcf_remove_filter,
-      [BcfHdr, Bcf1, :int, :int],
-      :int
-
-    # Returns 1 if present, 0 if absent, or -1 if filter does not exist.
-    # "PASS" and "." can be used interchangeably.
-    attach_function \
-      :bcf_has_filter,
-      [BcfHdr, Bcf1, :string],
-      :int
-
-    # Update REF and ALT column
-    attach_function \
-      :bcf_update_alleles,
-      [BcfHdr, Bcf1, :pointer, :int],
-      :int
-
-    attach_function \
-      :bcf_update_alleles_str,
-      [BcfHdr, Bcf1, :string],
-      :int
-
-    # Sets new ID string
-    attach_function \
-      :bcf_update_id,
-      [BcfHdr, Bcf1, :string],
-      :int
-
-    attach_function \
-      :bcf_add_id,
-      [BcfHdr, Bcf1, :string],
-      :int
-
-    # Functions for updating INFO fields
-    attach_function \
-      :bcf_update_info,
-      [BcfHdr, Bcf1, :string, :pointer, :int, :int],
-      :int
-
-    attach_function \
-      :bcf_update_format_string,
-      [BcfHdr, Bcf1, :string, :pointer, :int],
-      :int
-
-    # Functions for updating FORMAT fields
-    attach_function \
-      :bcf_update_format,
-      [BcfHdr, Bcf1, :string, :pointer, :int, :int],
-      :int
-
-    # Returns pointer to FORMAT's field data
-    attach_function \
-      :bcf_get_fmt,
-      [BcfHdr, Bcf1, :string],
-      BcfFmt.by_ref
-
-    attach_function \
-      :bcf_get_info,
-      [BcfHdr, Bcf1, :string],
-      BcfInfo.by_ref
-
-    # Returns pointer to FORMAT/INFO field data given the header index instead of the string ID
-    attach_function \
-      :bcf_get_fmt_id,
-      [Bcf1, :int],
-      BcfFmt.by_ref
-
-    attach_function \
-      :bcf_get_info_id,
-      [Bcf1, :int],
-      BcfInfo.by_ref
-
-    # get INFO values
-    attach_function \
-      :bcf_get_info_values,
-      [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
-      :int
-
-    attach_function \
-      :bcf_get_format_string,
-      [BcfHdr, Bcf1, :string, :pointer, :pointer],
-      :int
-
-    attach_function \
-      :bcf_get_format_values,
-      [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
-      :int
-
-    # Helper functions
-
-    # Translates string into numeric ID
-    attach_function \
-      :bcf_hdr_id2int,
-      [BcfHdr, :int, :string],
-      :int
-
-    # Convert BCF FORMAT data to string form
-    attach_function \
-      :bcf_fmt_array,
-      [KString, :int, :int, :pointer],
-      :int
-
-    attach_function \
-      :bcf_fmt_sized_array,
-      [KString, :pointer],
-      :uint8
-
-    # Encode a variable-length char array in BCF format
-    attach_function \
-      :bcf_enc_vchar,
-      [KString, :int, :string],
-      :int
-
-    # Encode a variable-length integer array in BCF format
-    attach_function \
-      :bcf_enc_vint,
-      [KString, :int, :pointer, :int],
-      :int
-
-    # Encode a variable-length float array in BCF format
-    attach_function \
-      :bcf_enc_vfloat,
-      [KString, :int, :pointer],
-      :int
-
-    # BCF index
-
-    # Load a BCF index from a given index file name
-    attach_function \
-      :bcf_index_load2,
-      %i[string string],
-      HtsIdx.by_ref
-
-    # Load a BCF index from a given index file name
-    attach_function \
-      :bcf_index_load3,
-      %i[string string int],
-      HtsIdx.by_ref
-
-    # Generate and save an index file
-    attach_function \
-      :bcf_index_build,
-      %i[string int],
-      :int
-
-    # Generate and save an index to a specific file
-    attach_function \
-      :bcf_index_build2,
-      %i[string string int],
-      :int
-
-    # Generate and save an index to a specific file
-    attach_function \
-      :bcf_index_build3,
-      %i[string string int int],
-      :int
-
-    # Initialise fp->idx for the current format type, for VCF and BCF files.
-    attach_function \
-      :bcf_idx_init,
-      [HtsFile, BcfHdr, :int, :string],
-      :int
-
-    # Writes the index initialised with bcf_idx_init to disk.
-    attach_function \
-      :bcf_idx_save,
-      [HtsFile],
-      :int
-
-    attach_variable \
-      :bcf_float_vector_end,
-      :uint32
-
-    attach_variable \
-      :bcf_float_missing,
-      :uint32
-
-    attach_function \
-      :bcf_format_gt_v2,
-      [BcfHdr, BcfFmt, :int, KString],
-      :int
-  end
-end
-
-require_relative "vcf_funcs"