htslib 0.4.2 → 0.5.0

data/lib/hts/libhts/vcf_funcs.rb

@@ -1,366 +0,0 @@
-# frozen_string_literal: true
-
-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
-      # Get number of samples
-      def bcf_hdr_nsamples(hdr)
-        hdr[:n][BCF_DT_SAMPLE]
-      end
-
-      # Function for updating INFO fields
-      def bcf_update_info_int32(hdr, line, key, values, n)
-        bcf_update_info(hdr, line, key, values, n, BCF_HT_INT)
-      end
-
-      # Function for updating INFO fields (int64; VCF only)
-      def bcf_update_info_int64(hdr, line, key, values, n)
-        bcf_update_info(hdr, line, key, values, n, BCF_HT_LONG)
-      end
-
-      # Function for updating INFO fields
-      def bcf_update_info_float(hdr, line, key, values, n)
-        bcf_update_info(hdr, line, key, values, n, BCF_HT_REAL)
-      end
-
-      # Function for updating INFO fields
-      def bcf_update_info_flag(hdr, line, key, string, n)
-        bcf_update_info(hdr, line, key, string, n, BCF_HT_FLAG)
-      end
-
-      # Function for updating INFO fields
-      def bcf_update_info_string(hdr, line, key, string)
-        bcf_update_info(hdr, line, key, string, 1, BCF_HT_STR)
-      end
-
-      # Function for updating FORMAT fields
-      def bcf_update_format_int32(hdr, line, key, values, n)
-        bcf_update_format(hdr, line, key, values, n,
-                          BCF_HT_INT)
-      end
-
-      # Function for updating FORMAT fields
-      def bcf_update_format_float(hdr, line, key, values, n)
-        bcf_update_format(hdr, line, key, values, n,
-                          BCF_HT_REAL)
-      end
-
-      # Function for updating FORMAT fields
-      def bcf_update_format_char(hdr, line, key, values, n)
-        bcf_update_format(hdr, line, key, values, n,
-                          BCF_HT_STR)
-      end
-
-      # Function for updating FORMAT fields
-      def bcf_update_genotypes(hdr, line, gts, n)
-        bcf_update_format(hdr, line, "GT", gts, n, BCF_HT_INT)
-      end
-
-      # Macro for setting genotypes correctly
-      def bcf_gt_phased(idx)
-        ((idx + 1) << 1 | 1)
-      end
-
-      # Macro for setting genotypes correctly
-      def bcf_gt_unphased(idx)
-        ((idx + 1) << 1)
-      end
-
-      # Macro for setting genotypes correctly
-      def bcf_gt_missing
-        0
-      end
-
-      # Macro for setting genotypes correctly
-      def bcf_gt_vector_end
-        bcf_int32_vector_end
-      end
-
-      # Macro for setting genotypes correctly
-      def bcf_gt_is_missing(val)
-        ((val >> 1) == 0 ? 1 : 0)
-      end
-
-      # Macro for setting genotypes correctly
-      def bcf_gt_is_vector_end(val)
-        val == bcf_gt_vector_end ? 1 : 0
-      end
-
-      # Macro for setting genotypes correctly
-      def bcf_gt_is_phased(idx)
-        (idx & 1)
-      end
-
-      # Macro for setting genotypes correctly
-      def bcf_gt_allele(val)
-        ((val >> 1) - 1)
-      end
-
-      # Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
-      def bcf_alleles2gt(a, b)
-        (a > b ? (a * (a + 1) / 2 + b) : (b * (b + 1) / 2 + a))
-      end
-
-      # Get INFO values
-      def bcf_get_info_int32(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_INT)
-      end
-
-      # Get INFO values (int64; VCF only)
-      def bcf_get_info_int64(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_LONG)
-      end
-
-      # Get INFO values
-      def bcf_get_info_float(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_REAL)
-      end
-
-      # Get INFO values
-      def bcf_get_info_string(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_STR)
-      end
-
-      # Get INFO values
-      def bcf_get_info_flag(hdr, line, tag, dst, ndst)
-        bcf_get_info_values(hdr, line, tag, dst, ndst, BCF_HT_FLAG)
-      end
-
-      # Get FORMAT values
-      def bcf_get_format_int32(hdr, line, tag, dst, ndst)
-        bcf_get_format_values(hdr, line, tag, dst, ndst, BCF_HT_INT)
-      end
-
-      # Get FORMAT values
-      def bcf_get_format_float(hdr, line, tag, dst, ndst)
-        bcf_get_format_values(hdr, line, tag, dst, ndst, BCF_HT_REAL)
-      end
-
-      # Get FORMAT values
-      def bcf_get_format_char(hdr, line, tag, dst, ndst)
-        bcf_get_format_values(hdr, line, tag, dst, ndst, BCF_HT_STR)
-      end
-
-      # Get FORMAT values
-      def bcf_get_genotypes(hdr, line, dst, ndst)
-        bcf_get_format_values(hdr, line, "GT", dst, ndst, BCF_HT_INT)
-      end
-
-      # Translates numeric ID into string
-      def bcf_hdr_int2id(hdr, type, int_id)
-        LibHTS::BcfIdpair.new(
-          hdr[:id][type].to_ptr +
-          LibHTS::BcfIdpair.size * int_id # offsets
-        )[:key]
-      end
-
-      # Translates sequence names (chromosomes) into numeric ID
-      def bcf_hdr_name2id(hdr, id)
-        bcf_hdr_id2int(hdr, BCF_DT_CTG, id)
-      end
-
-      # Translates numeric ID to sequence name
-      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
-
-      # Macro for accessing bcf_idinfo_t
-      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
-
-      # Macro for accessing bcf_idinfo_t
-      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
-
-      # Macro for accessing bcf_idinfo_t
-      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
-
-      # Macro for accessing bcf_idinfo_t
-      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
-
-      def bcf_hdr_idinfo_exists(hdr, type, int_id)
-        return false if int_id.negative? || int_id >= hdr[:n][LibHTS::BCF_DT_ID]
-
-        pair = LibHTS::BcfIdpair.new(
-          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
-          LibHTS::BcfIdpair.size * int_id # offset
-        )
-
-        !pair[:val].null? && bcf_hdr_id2coltype(hdr, type, int_id) != 0xf
-      end
-
-      # def bcf_hdr_id2hrec
-
-      alias bcf_itr_destroy hts_itr_destroy
-
-      def bcf_itr_queryi(idx, tid, beg, _end)
-        hts_itr_query(idx, tid, beg, _end, @ffi_functions[:bcf_readrec])
-      end
-
-      @@bcf_hdr_name2id = proc do |hdr, id|
-        LibHTS.bcf_hdr_name2id(hdr, id)
-      end
-
-      def bcf_itr_querys(idx, hdr, s)
-        return bcf_itr_querys1(idx, hdr, s) if respond_to?(:bcf_itr_querys1)
-
-        hts_itr_querys(idx, s, @@bcf_hdr_name2id, hdr, @ffi_functions[:hts_itr_query], @ffi_functions[:bcf_readrec])
-      end
-
-      # Ruby implementation of htslib's static inline bcf_itr_next().
-      def bcf_itr_next(htsfp, itr, r)
-        return -2 unless htsfp[:is_bgzf] == 1
-
-        if itr[:multi] == 1
-          hts_itr_multi_next(htsfp, itr, r)
-        else
-          hts_itr_next(htsfp[:fp][:bgzf], itr, r, FFI::Pointer::NULL)
-        end
-      end
-
-      # Load a BCF index
-      def bcf_index_load(fn)
-        hts_idx_load(fn, HTS_FMT_CSI)
-      end
-
-      # Load a BCF index
-      def bcf_index_seqnames(idx, hdr, nptr)
-        hts_idx_seqnames(idx, nptr, @@bcf_hdr_id2name, hdr)
-      end
-
-      # Typed value I/O
-      # INT8_MIN  + 1
-      def bcf_int8_vector_end  = -127
-      # INT16_MIN + 1
-      def bcf_int16_vector_end = -32_767
-      # INT32_MIN + 1
-      def bcf_int32_vector_end = -2_147_483_647
-      # INT64_MIN + 1
-      def bcf_int64_vector_end = -9_223_372_036_854_775_807
-      def bcf_str_vector_end   = 0
-      # INT8_MIN
-      def bcf_int8_missing     = -128
-      # INT16_MIN
-      def bcf_int16_missing    = (-32_767 - 1)
-      # INT32_MIN
-      def bcf_int32_missing    = (-2_147_483_647 - 1)
-      # INT64_MIN
-      def bcf_int64_missing    = (-9_223_372_036_854_775_807 - 1)
-      def bcf_str_missing      = 0x07
-
-      BCF_MAX_BT_INT8  = 0x7f           # INT8_MAX  */
-      BCF_MAX_BT_INT16 = 0x7fff         # INT16_MAX */
-      BCF_MAX_BT_INT32 = 0x7fffffff     # INT32_MAX */
-      BCF_MIN_BT_INT8  = -120           # INT8_MIN  + 8 */
-      BCF_MIN_BT_INT16 = -32_760        # INT16_MIN + 8 */
-      BCF_MIN_BT_INT32 = -2_147_483_640 # INT32_MIN + 8 */
-    end
-  end
-end

data/lib/hts/libhts.rb

@@ -1,47 +0,0 @@
-# frozen_string_literal: true
-
-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
-
-    begin
-      ffi_lib HTS.lib_path
-    rescue LoadError => e
-      raise LoadError, "#{e}\nCould not find #{HTS.lib_path}"
-    end
-
-    # @!macro attach_function
-    #   @!scope class
-    #   @!method $1(${2--2})
-    #   @return [${-1}] the return value of $0
-    def self.attach_function(*)
-      super
-    rescue FFI::NotFoundError => e
-      warn e.message if $VERBOSE
-    end
-
-    def self.attach_variable(*)
-      super
-    rescue FFI::NotFoundError => e
-      warn e.message if $VERBOSE
-    end
-  end
-end
-
-require_relative "libhts/constants"
-
-# This is alphabetical order.
-require_relative "libhts/kfunc"
-require_relative "libhts/bgzf"
-require_relative "libhts/hfile"
-require_relative "libhts/hts"
-require_relative "libhts/sam"
-require_relative "libhts/cram"
-require_relative "libhts/vcf"
-require_relative "libhts/tbx"
-require_relative "libhts/fai"
-require_relative "libhts/thread_pool"