htslib 0.1.0 → 0.2.0

data/lib/hts/libhts/vcf.rb

@@ -1,240 +1,439 @@
 # frozen_string_literal: true
 
-require_relative "vcf_funcs"
-
 module HTS
   module LibHTS
-    # constants
-    BCF_HL_FLT    = 0 # header line
-    BCF_HL_INFO   = 1
-    BCF_HL_FMT    = 2
-    BCF_HL_CTG    = 3
-    BCF_HL_STR    = 4 # structured header line TAG=<A=..,B=..>
-    BCF_HL_GEN    = 5 # generic header line
-
-    BCF_HT_FLAG   = 0 # header type
-    BCF_HT_INT    = 1
-    BCF_HT_REAL   = 2
-    BCF_HT_STR    = 3
-    BCF_HT_LONG   = (BCF_HT_INT | 0x100) # BCF_HT_INT, but for int64_t values; VCF only!
-
-    BCF_VL_FIXED  = 0 # variable length
-    BCF_VL_VAR    = 1
-    BCF_VL_A      = 2
-    BCF_VL_G      = 3
-    BCF_VL_R      = 4
-
-    BCF_DT_ID     = 0 # dictionary type
-    BCF_DT_CTG    = 1
-    BCF_DT_SAMPLE = 2
-
-    BCF_BT_NULL   = 0
-    BCF_BT_INT8   = 1
-    BCF_BT_INT16  = 2
-    BCF_BT_INT32  = 3
-    BCF_BT_INT64  = 4 # Unofficial, for internal use only.
-    BCF_BT_FLOAT  = 5
-    BCF_BT_CHAR   = 7
-
-    VCF_REF       = 0
-    VCF_SNP       = 1
-    VCF_MNP       = 2
-    VCF_INDEL     = 4
-    VCF_OTHER     = 8
-    VCF_BND       = 16 # breakend
-    VCF_OVERLAP   = 32 # overlapping deletion, ALT=*
-
-    BCF1_DIRTY_ID  = 1
-    BCF1_DIRTY_ALS = 2
-    BCF1_DIRTY_FLT = 4
-    BCF1_DIRTY_INF = 8
-
-    BCF_ERR_CTG_UNDEF   = 1
-    BCF_ERR_TAG_UNDEF   = 2
-    BCF_ERR_NCOLS       = 4
-    BCF_ERR_LIMITS      = 8
-    BCF_ERR_CHAR        = 16
-    BCF_ERR_CTG_INVALID = 32
-    BCF_ERR_TAG_INVALID = 64
-
-    # macros
-    class << self
-      alias bcf_init1    bcf_init
-      alias bcf_read1    bcf_read
-      alias vcf_read1    vcf_read
-      alias bcf_write1   bcf_write
-      alias vcf_write1   vcf_write
-      alias bcf_destroy1 bcf_destroy
-      alias bcf_empty1   bcf_empty
-      alias vcf_parse1   vcf_parse
-      alias bcf_clear1   bcf_clear
-      alias vcf_format1  vcf_format
-
-      alias bcf_open     hts_open
-      alias vcf_open     hts_open
-      if respond_to?(:hts_flush)
-        alias bcf_flush hts_flush
-        alias vcf_flush hts_flush
-      end
-      alias bcf_close    hts_close
-      alias vcf_close    hts_close
-    end
-
-    BCF_UN_STR  = 1 # up to ALT inclusive
-    BCF_UN_FLT  = 2 # up to FILTER
-    BCF_UN_INFO = 4 # up to INFO
-    BCF_UN_SHR  = (BCF_UN_STR | BCF_UN_FLT | BCF_UN_INFO) # all shared information
-    BCF_UN_FMT  = 8 # unpack format and each sample
-    BCF_UN_IND  = BCF_UN_FMT # a synonym of BCF_UN_FMT
-    BCF_UN_ALL  = (BCF_UN_SHR | BCF_UN_FMT) # everything
-
-    class << self
-      def bcf_hdr_nsamples(hdr)
-        hdr[:n][BCF_DT_SAMPLE]
-      end
-
-      def bcf_update_info_int32(hdr, line, key, values, n)
-        bcf_update_info(hdr, line, key, values, n, BCF_HT_INT)
-      end
-
-      def bcf_update_info_float(hdr, line, key, values, n)
-        bcf_update_info(hdr, line, key, values, n, BCF_HT_REAL)
-      end
-
-      def bcf_update_info_flag(hdr, line, key, string, n)
-        bcf_update_info(hdr, line, key, string, n, BCF_HT_FLAG)
-      end
-
-      def bcf_update_info_string(hdr, line, key, string)
-        bcf_update_info(hdr, line, key, string, 1, BCF_HT_STR)
-      end
-
-      def bcf_update_format_int32(hdr, line, key, values, n)
-        bcf_update_format(hdr, line, key, values, n,
-                          BCF_HT_INT)
-      end
-
-      def bcf_update_format_float(hdr, line, key, values, n)
-        bcf_update_format(hdr, line, key, values, n,
-                          BCF_HT_REAL)
-      end
-
-      def bcf_update_format_char(hdr, line, key, values, n)
-        bcf_update_format(hdr, line, key, values, n,
-                          BCF_HT_STR)
-      end
-
-      def bcf_update_genotypes(hdr, line, gts, n)
-        bcf_update_format(hdr, line, "GT", gts, n, BCF_HT_INT)
-      end
-
-      def bcf_gt_phased(idx)
-        ((idx + 1) << 1 | 1)
-      end
-
-      def bcf_gt_unphased(idx)
-        ((idx + 1) << 1)
-      end
-
-      def bcf_gt_missing
-        0
-      end
-
-      def bcf_gt_is_missing(val)
-        ((val) >> 1 ? 0 : 1)
-      end
-
-      def bcf_gt_is_phased(idx)
-        ((idx) & 1)
-      end
-
-      def bcf_gt_allele(val)
-        (((val) >> 1) - 1)
-      end
-
-      def bcf_alleles2gt(a, b)
-        ((a) > (b) ? (a * (a + 1) / 2 + b) : (b * (b + 1) / 2 + a))
-      end
-
-      def bcf_get_info_int32(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_INT)
-      end
-
-      def bcf_get_info_float(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_REAL)
-      end
-
-      def bcf_get_info_string(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_STR)
-      end
-
-      def bcf_get_info_flag(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_FLAG)
-      end
-
-      def bcf_get_format_int32(hdr, line, tag, dst, ndst)
-        bcf_get_format_values(hdr, line, tag, dst, ndst, BCF_HT_INT)
-      end
-
-      def bcf_get_format_float(hdr, line, tag, dst, ndst)
-        bcf_get_format_values(hdr, line, tag, dst, ndst, BCF_HT_REAL)
-      end
-
-      def bcf_get_format_char(hdr, line, tag, dst, ndst)
-        bcf_get_format_values(hdr, line, tag, dst, ndst, BCF_HT_STR)
-      end
-
-      def bcf_get_genotypes(hdr, line, dst, ndst)
-        bcf_get_format_values(hdr, line, "GT", dst, ndst, BCF_HT_INT)
-      end
-
-      def bcf_hdr_int2id(hdr, type, int_id)
-        LibHTS::BcfIdpair.new(
-          hdr[:id][type].to_ptr +
-          LibHTS::BcfIdpair.size * int_id # offsets
-        )[:key]
-      end
-
-      def bcf_hdr_name2id(hdr, id)
-        bcf_hdr_id2int(hdr, BCF_DT_CTG, id)
-      end
-
-      def bcf_hdr_id2name(hdr, rid)
-        return nil if hdr.null? || rid < 0 || rid >= hdr[:n][LibHTS::BCF_DT_CTG]
-
-        LibHTS::BcfIdpair.new(
-          hdr[:id][LibHTS::BCF_DT_CTG].to_ptr +
-          LibHTS::BcfIdpair.size * rid # offset
-        )[:key]
-      end
-
-      def bcf_hdr_id2length(hdr, type, int_id)
-        LibHTS::BcfIdpair.new(
-          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
-          LibHTS::BcfIdpair.size * int_id # offset
-        )[:val][:info][type] >> 8 & 0xf
-      end
-
-      def bcf_hdr_id2number(hdr, type, int_id)
-        LibHTS::BcfIdpair.new(
-          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
-          LibHTS::BcfIdpair.size * int_id # offset
-        )[:val][:info][type] >> 12
-      end
-
-      def bcf_hdr_id2type(hdr, type, int_id)
-        LibHTS::BcfIdpair.new(
-          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
-          LibHTS::BcfIdpair.size * int_id # offset
-        )[:val][:info][type] >> 4 & 0xf
-      end
-
-      def bcf_hdr_id2coltype(hdr, type, int_id)
-        LibHTS::BcfIdpair.new(
-          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
-          LibHTS::BcfIdpair.size * int_id # offset
-        )[:val][:info][type] & 0xf
-      end
-    end
+    attach_function \
+      :bcf_hdr_init,
+      [:string],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_destroy,
+      [BcfHdr],
+      :void
+
+    attach_function \
+      :bcf_init,
+      [],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_destroy,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_empty,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_clear,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_hdr_read,
+      [HtsFile],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_set_samples,
+      [BcfHdr, :string, :int],
+      :int
+
+    attach_function \
+      :bcf_subset_format,
+      [BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_hdr_write,
+      [HtsFile, BcfHdr],
+      :int
+
+    attach_function \
+      :vcf_parse,
+      [KString, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_open_mode,
+      %i[string string string],
+      :int
+
+    attach_function \
+      :vcf_format,
+      [BcfHdr, Bcf1, KString],
+      :int
+
+    attach_function \
+      :bcf_read,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_unpack,
+      [Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_dup,
+      [Bcf1],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_copy,
+      [Bcf1, Bcf1],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_write,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_hdr_read,
+      [HtsFile],
+      BcfHdr.by_ref
+
+    attach_function \
+      :vcf_hdr_write,
+      [HtsFile, BcfHdr],
+      :int
+
+    attach_function \
+      :vcf_read,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_write,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_readrec,
+      [BGZF, :pointer, :pointer, :pointer, :hts_pos_t, :hts_pos_t],
+      :int
+
+    attach_function \
+      :vcf_write_line,
+      [HtsFile, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_dup,
+      [BcfHdr],
+      BcfHdr.by_ref
+
+    # DEPRECATED
+    #
+    # attach_function \
+    #   :bcf_hdr_combine,
+    #   [BcfHdr, BcfHdr],
+    #   :int
+
+    attach_function \
+      :bcf_hdr_merge,
+      [BcfHdr, BcfHdr],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_add_sample,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_set,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_format,
+      [BcfHdr, :int, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_fmt_text,
+      [BcfHdr, :int, :pointer],
+      :string
+
+    attach_function \
+      :bcf_hdr_append,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_printf,
+      [BcfHdr, :string, :varargs],
+      :int
+
+    attach_function \
+      :bcf_hdr_get_version,
+      [BcfHdr],
+      :string
+
+    attach_function \
+      :bcf_hdr_set_version,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_remove,
+      [BcfHdr, :int, :string],
+      :void
+
+    attach_function \
+      :bcf_hdr_subset,
+      [BcfHdr, :int, :pointer, :pointer],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_seqnames,
+      [BcfHdr, :pointer],
+      :pointer
+
+    attach_function \
+      :bcf_hdr_parse,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_sync,
+      [BcfHdr],
+      :int
+
+    attach_function \
+      :bcf_hdr_parse_line,
+      [BcfHdr, :string, :pointer],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_format,
+      [BcfHrec, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_add_hrec,
+      [BcfHdr, BcfHrec],
+      :int
+
+    attach_function \
+      :bcf_hdr_get_hrec,
+      [BcfHdr, :int, :string, :string, :string],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_dup,
+      [BcfHrec],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_add_key,
+      [BcfHrec, :string, :size_t],
+      :int
+
+    attach_function \
+      :bcf_hrec_set_val,
+      [BcfHrec, :int, :string, :size_t, :int],
+      :int
+
+    attach_function \
+      :bcf_hrec_find_key,
+      [BcfHrec, :string],
+      :int
+
+    attach_function \
+      :hrec_add_idx,
+      [BcfHrec, :int],
+      :int
+
+    attach_function \
+      :bcf_hrec_destroy,
+      [BcfHrec],
+      :void
+
+    attach_function \
+      :bcf_subset,
+      [BcfHdr, Bcf1, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_translate,
+      [BcfHdr, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_get_variant_types,
+      [Bcf1],
+      :int
+
+    attach_function \
+      :bcf_get_variant_type,
+      [Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_is_snp,
+      [Bcf1],
+      :int
+
+    attach_function \
+      :bcf_update_filter,
+      [BcfHdr, Bcf1, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_add_filter,
+      [BcfHdr, Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_remove_filter,
+      [BcfHdr, Bcf1, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_has_filter,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_alleles,
+      [BcfHdr, Bcf1, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_update_alleles_str,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_id,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_add_id,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_info,
+      [BcfHdr, Bcf1, :string, :pointer, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_update_format_string,
+      [BcfHdr, Bcf1, :string, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_update_format,
+      [BcfHdr, Bcf1, :string, :pointer, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_get_fmt,
+      [BcfHdr, Bcf1, :string],
+      BcfFmt.by_ref
+
+    attach_function \
+      :bcf_get_info,
+      [BcfHdr, Bcf1, :string],
+      BcfInfo.by_ref
+
+    attach_function \
+      :bcf_get_fmt_id,
+      [Bcf1, :int],
+      BcfFmt.by_ref
+
+    attach_function \
+      :bcf_get_info_id,
+      [Bcf1, :int],
+      BcfInfo.by_ref
+
+    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
+
+    attach_function \
+      :bcf_hdr_id2int,
+      [BcfHdr, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_fmt_array,
+      [KString, :int, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_fmt_sized_array,
+      [KString, :pointer],
+      :uint8_t
+
+    attach_function \
+      :bcf_enc_vchar,
+      [KString, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_enc_vint,
+      [KString, :int, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_enc_vfloat,
+      [KString, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_index_load2,
+      %i[string string],
+      HtsIdx.by_ref
+
+    attach_function \
+      :bcf_index_load3,
+      %i[string string int],
+      HtsIdx.by_ref
+
+    attach_function \
+      :bcf_index_build,
+      %i[string int],
+      :int
+
+    attach_function \
+      :bcf_index_build2,
+      %i[string string int],
+      :int
+
+    attach_function \
+      :bcf_index_build3,
+      %i[string string int int],
+      :int
+
+    attach_function \
+      :bcf_idx_init,
+      [HtsFile, BcfHdr, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_idx_save,
+      [HtsFile],
+      :int
   end
 end
+
+require_relative "vcf_funcs"