htslib 0.0.4 → 0.0.8

data/lib/hts/libhts/vcf.rb

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require_relative "vcf_funcs"
+
 module HTS
   module LibHTS
     # constants
@@ -9,8 +11,8 @@ module HTS
     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_FLAG   = 0 # header type
     BCF_HT_INT    = 1
     BCF_HT_REAL   = 2
     BCF_HT_STR    = 3
@@ -57,11 +59,36 @@ module HTS
 
     # macros
     class << self
-      alias bcf_open hts_open
-      alias vcf_open hts_open
-      alias bcf_close hts_close
-      alias vcf_close hts_close
+      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
@@ -167,440 +194,33 @@ module HTS
           LibHTS::BcfIdpair.size * int_id # offsets
         )[:key]
       end
-    end
 
-    # constants
-    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
+      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]
 
-    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
-
-    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
+        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
+    end
   end
 end