htslib 0.0.10 → 0.2.1

data/lib/hts/libhts/sam_funcs.rb

@@ -2,595 +2,138 @@
 
 module HTS
   module LibHTS
-    # 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
-
-    # 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
-
-    # 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, :pointer, :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)
-      # FIXME: check if htsfp is compressed BGZF
-      raise("Null iterator") if itr.null?
-
-      # FIXME: check multi
-      hts_itr_next(htsfp[:fp][:bgzf], itr, r, htsfp)
+    # constants
+    BAM_CMATCH     = 0
+    BAM_CINS       = 1
+    BAM_CDEL       = 2
+    BAM_CREF_SKIP  = 3
+    BAM_CSOFT_CLIP = 4
+    BAM_CHARD_CLIP = 5
+    BAM_CPAD       = 6
+    BAM_CEQUAL     = 7
+    BAM_CDIFF      = 8
+    BAM_CBACK      = 9
+
+    BAM_CIGAR_STR = "MIDNSHP=XB"
+    BAM_CIGAR_SHIFT = 4
+    BAM_CIGAR_MASK  = 0xf
+    BAM_CIGAR_TYPE  = 0x3C1A7
+
+    # macros
+    class << self
+      def bam_cigar_op(c)
+        c & BAM_CIGAR_MASK
+      end
+
+      def bam_cigar_oplen(c)
+        c >> BAM_CIGAR_SHIFT
+      end
+
+      def bam_cigar_opchr(c)
+        "#{BAM_CIGAR_STR}??????"[bam_cigar_op(c)]
+      end
+
+      def bam_cigar_gen(l, o)
+        l << BAM_CIGAR_SHIFT | o
+      end
+
+      def bam_cigar_type(o)
+        BAM_CIGAR_TYPE >> (o << 1) & 3
+      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, Bam1],
-      :int
-
-    attach_function \
-      :sam_format1,
-      [SamHdr, Bam1, KString],
-      :int
-
-    # Read a record from a file
-    attach_function \
-      :sam_read1,
-      [HtsFile, SamHdr, Bam1],
-      :int
-
-    # Write a record to a file
-    attach_function \
-      :sam_write1,
-      [HtsFile, SamHdr, Bam1],
-      :int
-
-    # Return a pointer to an aux record
-    attach_function \
-      :bam_aux_get,
-      [Bam1, :string], # FIXME
-      :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, :string, :int, :pointer],
-      :int
-
-    # Delete tag data from a bam record
-    attach_function \
-      :bam_aux_del,
-      [Bam1, :pointer],
-      :int
-
-    # 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],
-      :int
-
-    attach_function \
-      :bam_plp_next,
-      %i[bam_plp pointer pointer pointer],
-      BamPileup1.by_ref
-
-    attach_function \
-      :bam_plp_auto,
-      %i[bam_plp pointer pointer pointer],
-      BamPileup1.by_ref
-
-    attach_function \
-      :bam_plp64_next,
-      %i[bam_plp pointer pointer pointer],
-      BamPileup1.by_ref
-
-    attach_function \
-      :bam_plp64_auto,
-      %i[bam_plp 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
-
-    # sets a callback to initialise any per-pileup1_t fields.
-    attach_function \
-      :bam_plp_insertion,
-      [BamPileup1, KString, :pointer],
-      :int
-
-    # sets a callback to initialise any per-pileup1_t fields.
-    # bam_plp_constructor
-
-    # bam_plp_destructor
-
-    # Get pileup padded insertion sequence
-    # bam_plp_insertion
-
-    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
-
-    # bam_mplp_constructor
-    # bam_mplp_destructor
-
-    attach_function \
-      :sam_cap_mapq,
-      [Bam1, :string, :hts_pos_t, :int],
-      :int
-
-    attach_function \
-      :sam_prob_realn,
-      [Bam1, :string, :hts_pos_t, :int],
-      :int
+    BAM_FPAIRED        =    1
+    BAM_FPROPER_PAIR   =    2
+    BAM_FUNMAP         =    4
+    BAM_FMUNMAP        =    8
+    BAM_FREVERSE       =   16
+    BAM_FMREVERSE      =   32
+    BAM_FREAD1         =   64
+    BAM_FREAD2         =  128
+    BAM_FSECONDARY     =  256
+    BAM_FQCFAIL        =  512
+    BAM_FDUP           = 1024
+    BAM_FSUPPLEMENTARY = 2048
+
+    # macros
+    # function-like macros
+    class << self
+      def bam_is_rev(b)
+        b[:core][:flag] & BAM_FREVERSE != 0
+      end
+
+      def bam_is_mrev(b)
+        b[:core][:flag] & BAM_FMREVERSE != 0
+      end
+
+      def bam_get_qname(b)
+        b[:data]
+      end
+
+      def bam_get_cigar(b)
+        b[:data] + b[:core][:l_qname]
+      end
+
+      def bam_get_seq(b)
+        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname]
+      end
+
+      def bam_get_qual(b)
+        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] + ((b[:core][:l_qseq] + 1) >> 1)
+      end
+
+      def bam_get_aux(b)
+        b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] + ((b[:core][:l_qseq] + 1) >> 1) + b[:core][:l_qseq]
+      end
+
+      def bam_get_l_aux(b)
+        b[:l_data] - (b[:core][:n_cigar] << 2) - b[:core][:l_qname] - b[:core][:l_qseq] - ((b[:core][:l_qseq] + 1) >> 1)
+      end
+
+      def bam_seqi(s, i)
+        s[i >> 1].read_uint8 >> ((~i & 1) << 2) & 0xf
+      end
+
+      def bam_set_seqi(s, i, b)
+        s[i >> 1] = (s[i >> 1] & (0xf0 >> ((~i & 1) << 2))) | ((b) << ((~i & 1) << 2))
+      end
+
+      def sam_hdr_find_hd(h, ks)
+        sam_hdr_find_line_id(h, "HD", nil, nil, ks)
+      end
+
+      def sam_hdr_find_tag_hd(h, key, ks)
+        sam_hdr_find_tag_id(h, "HD", nil, nil, key, ks)
+      end
+
+      def sam_hdr_update_hd(h, *args)
+        sam_hdr_update_line(h, "HD", nil, nil, *args, nil)
+      end
+
+      def sam_hdr_remove_tag_hd(h, key)
+        sam_hdr_remove_tag_id(h, "HD", nil, nil, key)
+      end
+
+      BAM_USER_OWNS_STRUCT = 1
+      BAM_USER_OWNS_DATA   = 2
+
+      alias bam_itr_destroy hts_itr_destroy
+      alias bam_itr_queryi sam_itr_queryi
+      alias bam_itr_querys sam_itr_querys
+      alias bam_itr_next sam_itr_next
+
+      def bam_index_load(fn)
+        hts_idx_load(fn, HTS_FMT_BAI)
+      end
+
+      alias bam_index_build sam_index_build
+
+      alias sam_itr_destroy hts_itr_destroy
+
+      alias sam_open hts_open
+      alias sam_open_format hts_open_format
+      alias sam_flush hts_flush
+      alias sam_close hts_close
+    end
   end
 end