htslib 0.1.0 → 0.2.0

data/lib/hts/libhts/vcf_funcs.rb

@@ -2,429 +2,237 @@
 
 module HTS
   module LibHTS
-    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
+    # 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
   end
 end

data/lib/hts/libhts.rb

@@ -4,6 +4,7 @@ require_relative "ffi_ext/struct"
 require_relative "ffi_ext/pointer"
 
 module HTS
+  # A Module for working with native C HTSlib structures and functions.
   module LibHTS
     extend FFI::Library
 

data/lib/hts/tbx.rb

@@ -37,10 +37,9 @@ module HTS
 
       raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
 
-      if threads&.> 0
-        r = LibHTS.hts_set_threads(@hts_file, threads)
-        raise "Failed to set number of threads: #{threads}" if r < 0
-      end
+      set_threads(threads) if threads
+
+      super # do nothing
     end
   end
 end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
 end