htslib 0.4.1 → 0.5.0

data/lib/hts/libhts/sam.rb

@@ -1,760 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module LibHTS
-    # Callback type for bam_plp_auto_f: int (*)(void *data, bam1_t *b)
-    # Use raw pointer for bam1_t to avoid creating ManagedStruct wrappers (which would double-free)
-    callback :bam_plp_auto_f, %i[pointer pointer], :int
-    # callback :bam_plp_auto_f, [:pointer, Bam1.by_ref], :int
-
-    # Generates a new unpopulated header structure.
-    attach_function \
-      :sam_hdr_init,
-      [],
-      SamHdr.by_ref
-
-    # Read the header from a BAM compressed file.
-    attach_function \
-      :bam_hdr_read,
-      [BGZF],
-      SamHdr.by_ref
-
-    # Writes the header to a BAM file.
-    attach_function \
-      :bam_hdr_write,
-      [BGZF, SamHdr],
-      :int
-
-    # Frees the resources associated with a header.
-    attach_function \
-      :sam_hdr_destroy,
-      [SamHdr],
-      :void
-
-    # Duplicate a header structure.
-    attach_function \
-      :sam_hdr_dup,
-      [SamHdr],
-      SamHdr.by_ref
-
-    # Create a header from existing text.
-    attach_function \
-      :sam_hdr_parse,
-      %i[size_t string],
-      SamHdr.by_ref
-
-    # Read a header from a SAM, BAM or CRAM file.
-    attach_function \
-      :sam_hdr_read,
-      [SamFile],
-      SamHdr.by_ref
-
-    # Write a header to a SAM, BAM or CRAM file.
-    attach_function \
-      :sam_hdr_write,
-      [SamFile, SamHdr],
-      :int
-
-    # Returns the current length of the header text.
-    attach_function \
-      :sam_hdr_length,
-      [SamHdr],
-      :size_t
-
-    # Returns the text representation of the header.
-    attach_function \
-      :sam_hdr_str,
-      [SamHdr],
-      :string
-
-    # Returns the number of references in the header.
-    attach_function \
-      :sam_hdr_nref,
-      [SamHdr],
-      :int
-
-    # Add formatted lines to an existing header.
-    attach_function \
-      :sam_hdr_add_lines,
-      [SamHdr, :string, :size_t],
-      :int
-
-    # Adds a single line to an existing header.
-    attach_function \
-      :sam_hdr_add_line,
-      [SamHdr, :string, :varargs],
-      :int
-
-    # Returns a complete line of formatted text for a given type and ID.
-    attach_function \
-      :sam_hdr_find_line_id,
-      [SamHdr, :string, :string, :string, KString],
-      :int
-
-    # Returns a complete line of formatted text for a given type and index.
-    attach_function \
-      :sam_hdr_find_line_pos,
-      [SamHdr, :string, :int, KString],
-      :int
-
-    # Remove a line with given type / id from a header
-    attach_function \
-      :sam_hdr_remove_line_id,
-      [SamHdr, :string, :string, :string],
-      :int
-
-    # Remove nth line of a given type from a header
-    attach_function \
-      :sam_hdr_remove_line_pos,
-      [SamHdr, :string, :int],
-      :int
-
-    # Add or update tag key,value pairs in a header line.
-    attach_function \
-      :sam_hdr_update_line,
-      [SamHdr, :string, :string, :string, :varargs],
-      :int
-
-    # Remove all lines of a given type from a header, except the one matching an ID
-    attach_function \
-      :sam_hdr_remove_except,
-      [SamHdr, :string, :string, :string],
-      :int
-
-    # Remove header lines of a given type, except those in a given ID set
-    attach_function \
-      :sam_hdr_remove_lines,
-      [SamHdr, :string, :string, :pointer],
-      :int
-
-    # Count the number of lines for a given header type
-    attach_function \
-      :sam_hdr_count_lines,
-      [SamHdr, :string],
-      :int
-
-    # Index of the line for the types that have dedicated look-up tables (SQ, RG, PG)
-    attach_function \
-      :sam_hdr_line_index,
-      [SamHdr, :string, :string],
-      :int
-
-    # Id key of the line for the types that have dedicated look-up tables (SQ, RG, PG)
-    attach_function \
-      :sam_hdr_line_name,
-      [SamHdr, :string, :int],
-      :string
-
-    # Return the value associated with a key for a header line identified by ID_key:ID_val
-    attach_function \
-      :sam_hdr_find_tag_id,
-      [SamHdr, :string, :string, :string, :string, KString],
-      :int
-
-    # Return the value associated with a key for a header line identified by position
-    attach_function \
-      :sam_hdr_find_tag_pos,
-      [SamHdr, :string, :int, :string, KString],
-      :int
-
-    # Remove the key from the line identified by type, ID_key and ID_value.
-    attach_function \
-      :sam_hdr_remove_tag_id,
-      [SamHdr, :string, :string, :string, :string],
-      :int
-
-    # Get the target id for a given reference sequence name
-    attach_function \
-      :sam_hdr_name2tid,
-      [SamHdr, :string],
-      :int
-
-    # Get the reference sequence name from a target index
-    attach_function \
-      :sam_hdr_tid2name,
-      [SamHdr, :int],
-      :string
-
-    # Get the reference sequence length from a target index
-    attach_function \
-      :sam_hdr_tid2len,
-      [SamHdr, :int],
-      :hts_pos_t
-
-    # Generate a unique \@PG ID: value
-    attach_function \
-      :sam_hdr_pg_id,
-      [SamHdr, :string],
-      :string
-
-    # Add an \@PG line.
-    attach_function \
-      :sam_hdr_add_pg,
-      [SamHdr, :string, :varargs],
-      :int
-
-    # A function to help with construction of CL tags in @PG records.
-    attach_function \
-      :stringify_argv,
-      %i[int pointer],
-      :string
-
-    # Increments the reference count on a header
-    attach_function \
-      :sam_hdr_incr_ref,
-      [SamHdr],
-      :void
-
-    # Create a new bam1_t alignment structure
-    attach_function \
-      :bam_init1,
-      [],
-      Bam1.by_ref
-
-    # Destroy a bam1_t structure
-    attach_function \
-      :bam_destroy1,
-      [Bam1],
-      :void
-
-    # Read a BAM format alignment record
-    attach_function \
-      :bam_read1,
-      [BGZF, Bam1],
-      :int
-
-    # Write a BAM format alignment record
-    attach_function \
-      :bam_write1,
-      [BGZF, Bam1],
-      :int
-
-    # Copy alignment record data
-    attach_function \
-      :bam_copy1,
-      [Bam1, Bam1],
-      Bam1.by_ref
-
-    # Create a duplicate alignment record
-    attach_function \
-      :bam_dup1,
-      [Bam1],
-      Bam1.by_ref
-
-    # Set all components of an alignment structure
-    attach_function \
-      :bam_set1,
-      [Bam1,
-       :size_t,
-       :string,
-       :uint16,
-       :int32,
-       :hts_pos_t,
-       :uint8,
-       :size_t,
-       :pointer,
-       :int32,
-       :hts_pos_t,
-       :hts_pos_t,
-       :size_t,
-       :string,
-       :string,
-       :size_t],
-      :int
-
-    # Calculate query length from CIGAR data
-    attach_function \
-      :bam_cigar2qlen,
-      %i[int pointer],
-      :int64
-
-    # Calculate reference length from CIGAR data
-    attach_function \
-      :bam_cigar2rlen,
-      %i[int pointer],
-      :hts_pos_t
-
-    # Calculate the rightmost base position of an alignment on the reference genome.
-    attach_function \
-      :bam_endpos,
-      [Bam1],
-      :hts_pos_t
-
-    attach_function \
-      :bam_str2flag,
-      [:string],
-      :int
-
-    attach_function \
-      :bam_flag2str,
-      [:int],
-      :string
-
-    # Set the name of the query
-    attach_function \
-      :bam_set_qname,
-      [Bam1, :string],
-      :int
-
-    # Parse a CIGAR string into a uint32_t array
-    attach_function \
-      :sam_parse_cigar,
-      %i[string pointer pointer pointer],
-      :ssize_t
-
-    # Parse a CIGAR string into a bam1_t struct
-    attach_function \
-      :bam_parse_cigar,
-      [:string, :pointer, Bam1],
-      :ssize_t
-
-    # Initialise fp->idx for the current format type for SAM, BAM and CRAM types .
-    attach_function \
-      :sam_idx_init,
-      [HtsFile, SamHdr, :int, :string],
-      :int
-
-    # Writes the index initialised with sam_idx_init to disk.
-    attach_function \
-      :sam_idx_save,
-      [HtsFile],
-      :int
-
-    # Load a BAM (.csi or .bai) or CRAM (.crai) index file
-    attach_function \
-      :sam_index_load,
-      [HtsFile, :string],
-      HtsIdx.by_ref
-
-    # Load a specific BAM (.csi or .bai) or CRAM (.crai) index file
-    attach_function \
-      :sam_index_load2,
-      [HtsFile, :string, :string],
-      HtsIdx.by_ref
-
-    # Load or stream a BAM (.csi or .bai) or CRAM (.crai) index file
-    attach_function \
-      :sam_index_load3,
-      [HtsFile, :string, :string, :int],
-      HtsIdx.by_ref
-
-    # Generate and save an index file
-    attach_function \
-      :sam_index_build,
-      %i[string int],
-      :int
-
-    # Generate and save an index to a specific file
-    attach_function \
-      :sam_index_build2,
-      %i[string string int],
-      :int
-
-    # Generate and save an index to a specific file
-    attach_function \
-      :sam_index_build3,
-      %i[string string int int],
-      :int
-
-    # Create a BAM/CRAM iterator
-    attach_function \
-      :sam_itr_queryi,
-      [HtsIdx, :int, :hts_pos_t, :hts_pos_t],
-      HtsItr.by_ref
-
-    # Create a SAM/BAM/CRAM iterator
-    attach_function \
-      :sam_itr_querys,
-      [HtsIdx, SamHdr, :string],
-      HtsItr.by_ref
-
-    # Create a multi-region iterator
-    attach_function \
-      :sam_itr_regions,
-      [HtsIdx, SamHdr, HtsReglist, :uint],
-      HtsItr.by_ref
-
-    # Create a multi-region iterator
-    attach_function \
-      :sam_itr_regarray,
-      [HtsIdx, SamHdr, :pointer, :uint],
-      HtsItr.by_ref
-
-    # Get the next read from a SAM/BAM/CRAM iterator
-    def self.sam_itr_next(htsfp, itr, r)
-      raise("#{htsfp[:fn] || 'File'} not BGZF compressed") unless htsfp[:is_bgzf] == 1 || htsfp[:is_cram] == 1
-      raise("Null iterator") if itr.null?
-
-      if itr[:multi] == 1
-        hts_itr_multi_next(htsfp, itr, r)
-      else
-        bgzf = htsfp[:is_bgzf] == 1 ? htsfp[:fp][:bgzf] : FFI::Pointer::NULL
-        hts_itr_next(bgzf, itr, r, htsfp)
-      end
-    end
-
-    attach_function \
-      :sam_parse_region,
-      [SamHdr, :string, :pointer, :pointer, :pointer, :int],
-      :string
-
-    # SAM I/O
-
-    # macros (or alias)
-    # sam_open
-    # sam_open_format
-    # sam_close
-
-    attach_function \
-      :sam_open_mode,
-      %i[string string string],
-      :int
-
-    # A version of sam_open_mode that can handle ,key=value options.
-    attach_function \
-      :sam_open_mode_opts,
-      %i[string string string],
-      :string
-
-    attach_function \
-      :sam_hdr_change_HD,
-      [SamHdr, :string, :string],
-      :int
-
-    attach_function \
-      :sam_parse1,
-      [KString, SamHdr, :pointer], # [KString, SamHdr, (Bam1 | Bam1View)]
-      :int
-
-    attach_function \
-      :sam_format1,
-      [SamHdr, :pointer, KString], # [SamHdr, (Bam1 | Bam1View), KString]
-      :int
-
-    # Read a record from a file
-    attach_function \
-      :sam_read1,
-      [HtsFile, SamHdr, :pointer], # [HtsFile, SamHdr, (Bam1 | Bam1View)]
-      :int
-
-    # Write a record to a file
-    attach_function \
-      :sam_write1,
-      [HtsFile, SamHdr, :pointer], # [HtsFile, SamHdr, (Bam1 | Bam1View)]
-      :int
-
-    # Checks whether a record passes an hts_filter.
-    attach_function \
-      :sam_passes_filter,
-      [SamHdr, Bam1, :pointer], # hts_filter_t
-      :int
-
-    # Return a pointer to a BAM record's first aux field
-    attach_function \
-      :bam_aux_first,
-      [Bam1],
-      :pointer
-
-    # Return a pointer to a BAM record's next aux field
-    attach_function \
-      :bam_aux_next,
-      [Bam1, :pointer],
-      :pointer
-
-    # Return a pointer to an aux record
-    attach_function \
-      :bam_aux_get,
-      [Bam1, :string], # const char tag[2]
-      :pointer
-
-    # Get an integer aux value
-    attach_function \
-      :bam_aux2i,
-      [:pointer],
-      :int64
-
-    # Get an integer aux value
-    attach_function \
-      :bam_aux2f,
-      [:pointer],
-      :double
-
-    # Get a character aux value
-    attach_function \
-      :bam_aux2A,
-      [:pointer],
-      :char
-
-    # Get a string aux value
-    attach_function \
-      :bam_aux2Z,
-      [:pointer],
-      :string
-
-    # Get the length of an array-type ('B') tag
-    attach_function \
-      :bam_auxB_len,
-      [:pointer],
-      :uint
-
-    # Get an integer value from an array-type tag
-    attach_function \
-      :bam_auxB2i,
-      %i[pointer uint],
-      :int64
-
-    # Get a floating-point value from an array-type tag
-    attach_function \
-      :bam_auxB2f,
-      %i[pointer uint],
-      :double
-
-    # Append tag data to a bam record
-    attach_function \
-      :bam_aux_append,
-      [Bam1, :string, :char, :int, :pointer],
-      :int
-
-    # Delete tag data from a bam record
-    attach_function \
-      :bam_aux_del,
-      [Bam1, :pointer],
-      :int
-
-    # Delete an aux field from a BAM record. Identical to @c bam_aux_del() apart from the return value
-    attach_function \
-      :bam_aux_remove,
-      [Bam1, :pointer],
-      :pointer
-
-    # Update or add a string-type tag
-    attach_function \
-      :bam_aux_update_str,
-      [Bam1, :string, :int, :string],
-      :int
-
-    # Update or add an integer tag
-    attach_function \
-      :bam_aux_update_int,
-      [Bam1, :string, :int64],
-      :int
-
-    # Update or add a floating-point tag
-    attach_function \
-      :bam_aux_update_float,
-      [Bam1, :string, :float],
-      :int
-
-    # Update or add an array tag
-    attach_function \
-      :bam_aux_update_array,
-      [Bam1, :string, :uint8, :uint32, :pointer],
-      :int
-
-    # sets an iterator over multiple
-    attach_function \
-      :bam_plp_init,
-      %i[bam_plp_auto_f pointer],
-      :bam_plp
-
-    attach_function \
-      :bam_plp_destroy,
-      [:bam_plp],
-      :void
-
-    attach_function \
-      :bam_plp_push,
-      [:bam_plp, Bam1.by_ref],
-      :int
-
-    attach_function \
-      :bam_plp_next,
-      %i[bam_plp pointer pointer pointer],
-      :pointer # BamPileup1.by_ref
-
-    attach_function \
-      :bam_plp_auto,
-      %i[bam_plp pointer pointer pointer],
-      :pointer # BamPileup1.by_ref
-
-    attach_function \
-      :bam_plp64_next,
-      %i[bam_plp pointer pointer pointer],
-      :pointer # BamPileup1.by_ref
-
-    attach_function \
-      :bam_plp64_auto,
-      %i[bam_plp pointer pointer pointer],
-      :pointer # BamPileup1.by_ref
-
-    attach_function \
-      :bam_plp_set_maxcnt,
-      %i[bam_plp int],
-      :void
-
-    attach_function \
-      :bam_plp_reset,
-      [:bam_plp],
-      :void
-
-    # Callback type for constructor/destructor: int (*)(void *data, const bam1_t *b, bam_pileup_cd *cd)
-    callback :bam_plp_callback_function, [:pointer, :pointer, BamPileupCd.by_ref], :int
-    # callback :bam_plp_callback_function, [:pointer, Bam1.by_ref, BamPileupCd.by_ref], :int
-
-    # sets a callback to initialise any per-pileup1_t fields.
-    attach_function \
-      :bam_plp_constructor,
-      %i[bam_plp bam_plp_callback_function],
-      :void
-
-    attach_function \
-      :bam_plp_destructor,
-      %i[bam_plp bam_plp_callback_function],
-      :void
-
-    # Get pileup padded insertion sequence
-    # Make pointer passing explicit by using by_ref for structs
-    attach_function \
-      :bam_plp_insertion,
-      [BamPileup1.by_ref, KString.by_ref, :pointer],
-      :int
-
-    # Get pileup padded insertion sequence, including base modifications
-    attach_function \
-      :bam_plp_insertion_mod,
-      [BamPileup1.by_ref, HtsBaseModState, KString.by_ref, :pointer],
-      :int
-
-    # NOTE: There is no bam_plp_init_overlaps in HTSlib (only bam_mplp_init_overlaps exists).
-    # The incorrect binding is removed to avoid undefined symbol errors.
-
-    attach_function \
-      :bam_mplp_init,
-      %i[int bam_plp_auto_f pointer],
-      :bam_mplp
-
-    attach_function \
-      :bam_mplp_init_overlaps,
-      [:bam_mplp],
-      :int
-
-    attach_function \
-      :bam_mplp_destroy,
-      [:bam_mplp],
-      :void
-
-    attach_function \
-      :bam_mplp_set_maxcnt,
-      %i[bam_mplp int],
-      :void
-
-    attach_function \
-      :bam_mplp_auto,
-      %i[bam_mplp pointer pointer pointer pointer], # BamPileup1T
-      :int
-
-    attach_function \
-      :bam_mplp64_auto,
-      %i[bam_mplp pointer pointer pointer pointer], # BamPileup1T
-      :int
-
-    attach_function \
-      :bam_mplp_reset,
-      [:bam_mplp],
-      :void
-
-    attach_function \
-      :bam_mplp_constructor,
-      %i[bam_mplp bam_plp_callback_function],
-      :void
-
-    attach_function \
-      :bam_mplp_destructor,
-      %i[bam_mplp bam_plp_callback_function],
-      :void
-
-    attach_function \
-      :sam_cap_mapq,
-      [Bam1, :string, :hts_pos_t, :int],
-      :int
-
-    attach_function \
-      :sam_prob_realn,
-      [Bam1, :string, :hts_pos_t, :int],
-      :int
-
-    # Allocates an hts_base_mode_state.
-    attach_function \
-      :hts_base_mod_state_alloc,
-      [],
-      HtsBaseModState
-
-    # Destroys an  hts_base_mode_state.
-    attach_function \
-      :hts_base_mod_state_free,
-      [HtsBaseModState],
-      :void
-
-    # Parses the MM and ML tags out of a bam record.
-    attach_function \
-      :bam_parse_basemod,
-      [Bam1, HtsBaseModState],
-      :int
-
-    # Parses the MM and ML tags out of a bam record.
-    attach_function \
-      :bam_parse_basemod2,
-      [Bam1, HtsBaseModState, :uint32],
-      :int
-
-    # Returns modification status for the next base position in the query seq.
-    attach_function \
-      :bam_mods_at_next_pos,
-      [Bam1, HtsBaseModState, :pointer, :int],
-      :int
-
-    # Finds the next location containing base modifications and returns them
-    attach_function \
-      :bam_next_basemod,
-      [Bam1, HtsBaseModState, :pointer, :int, :pointer],
-      :int
-
-    # Returns modification status for a specific query position.
-    attach_function \
-      :bam_mods_at_qpos,
-      [Bam1, :int, HtsBaseModState, :pointer, :int],
-      :int
-
-    # Returns data about a specific modification type for the alignment record.
-    attach_function \
-      :bam_mods_query_type,
-      [HtsBaseModState, :int, :pointer, :pointer, :pointer],
-      :int
-
-    # Returns data about the i^th modification type for the alignment record.
-    attach_function \
-      :bam_mods_queryi,
-      [HtsBaseModState, :int, :pointer, :pointer, :pointer],
-      :int
-
-    # Returns the list of base modification codes provided for this
-    attach_function \
-      :bam_mods_recorded,
-      [HtsBaseModState, :pointer],
-      :pointer
-
-    # Sets the header to the file
-    attach_function \
-      :sam_hdr_set,
-      [HtsFile, SamHdr, :int],
-      :int
-
-    # Get the header from the file pointer
-    attach_function \
-      :sam_hdr_get,
-      [HtsFile],
-      SamHdr
-  end
-end
-
-require_relative "sam_funcs"