htslib 0.0.2 → 0.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +25 -16
- data/lib/hts/bam.rb +38 -32
- data/lib/hts/bam/cigar.rb +3 -3
- data/lib/hts/bam/flag.rb +91 -0
- data/lib/hts/bam/header.rb +2 -2
- data/lib/hts/bam/{alignment.rb → record.rb} +49 -43
- data/lib/hts/fai.rb +8 -8
- data/lib/hts/libhts.rb +141 -0
- data/lib/hts/{ffi → libhts}/bgzf.rb +1 -1
- data/lib/hts/{ffi → libhts}/constants.rb +114 -43
- data/lib/hts/{ffi → libhts}/faidx.rb +1 -1
- data/lib/hts/{ffi → libhts}/hfile.rb +1 -1
- data/lib/hts/{ffi → libhts}/hts.rb +7 -1
- data/lib/hts/{ffi → libhts}/kfunc.rb +1 -1
- data/lib/hts/{ffi → libhts}/sam.rb +25 -25
- data/lib/hts/{ffi → libhts}/tbx.rb +1 -1
- data/lib/hts/{ffi → libhts}/vcf.rb +1 -1
- data/lib/hts/vcf.rb +17 -17
- data/lib/hts/vcf/format.rb +24 -0
- data/lib/hts/vcf/header.rb +2 -2
- data/lib/hts/vcf/info.rb +24 -0
- data/lib/hts/vcf/{variant.rb → record.rb} +2 -2
- data/lib/hts/version.rb +1 -1
- data/lib/htslib.rb +16 -19
- metadata +20 -17
- data/lib/hts/ffi.rb +0 -85
data/lib/hts/fai.rb
CHANGED
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@@ -18,30 +18,30 @@ module HTS
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def initialize(path)
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@path = File.expand_path(path)
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-
@path.delete_suffix!(
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-
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-
@fai =
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@path.delete_suffix!(".fai")
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LibHTS.fai_build(@path) unless File.exist?("#{@path}.fai")
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@fai = LibHTS.fai_load(@path)
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raise if @fai.null?
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-
# at_exit{
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# at_exit{LibHTS.fai_destroy(@fai)}
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end
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def close
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-
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LibHTS.fai_destroy(@fai)
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end
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# the number of sequences in the index.
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def size
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-
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+
LibHTS.faidx_nseq(@fai)
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end
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alias length size
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# return the length of the requested chromosome.
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def chrom_size(chrom)
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raise ArgumentError,
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raise ArgumentError, "Expect chrom to be String or Symbol" unless chrom.is_a?(String) || chrom.is_a?(Symbol)
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chrom = chrom.to_s
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-
result =
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result = LibHTS.faidx_seq_len(@fai, chrom)
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result == -1 ? nil : result
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end
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alias chrom_length chrom_size
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data/lib/hts/libhts.rb
ADDED
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@@ -0,0 +1,141 @@
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# frozen_string_literal: true
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module HTS
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module LibHTS
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extend FFI::Library
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begin
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ffi_lib HTS.lib_path
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rescue LoadError => e
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raise LoadError, "#{e}\nCould not find #{HTS.lib_path}"
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end
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def self.attach_function(*)
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super
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rescue FFI::NotFoundError => e
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warn e.message
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end
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end
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end
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module FFI
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class Struct
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class << self
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# @example HtsOpt
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# class HtsOpt < FFI::Struct
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# layout \
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# :arg, :string,
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# :opt, HtsFmtOption,
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# :val,
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# union_layout(
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# :i, :int,
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# :s, :string
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# ),
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# :next, HtsOpt.ptr
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# end
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def union_layout(*args)
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Class.new(FFI::Union) { layout(*args) }
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end
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# @example HtsFormat
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# class HtsFormat < FFI::Struct
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# layout \
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# :category, HtsFormatCategory,
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# :format, HtsExactFormat,
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# :version,
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# struct_layout(
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# :major, :short,
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# :minor, :short
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# ),
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# :compression, HtsCompression,
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# :compression_level, :short,
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# :specific, :pointer
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# end
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def struct_layout(*args)
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Class.new(FFI::Struct) { layout(*args) }
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end
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end
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end
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# Struct that support bit fields.
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# Currently readonly.
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class BitStruct < Struct
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class << self
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module BitFieldsModule
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def [](name)
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bit_fields = self.class.bit_fields_hash_table
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parent, start, width = bit_fields[name]
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if parent
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(super(parent) >> start) & ((1 << width) - 1)
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else
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super(name)
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end
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end
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end
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private_constant :BitFieldsModule
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attr_reader :bit_fields_hash_table
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# @example Bcf1
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# class Bcf1 < FFI::BitStruct
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# layout \
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# :pos, :hts_pos_t,
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# :rlen, :hts_pos_t,
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# :rid, :int32_t,
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# :qual, :float,
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# :_n_info_allele, :uint32_t,
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# :_n_fmt_sample, :uint32_t,
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# :shared, KString,
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# :indiv, KString,
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# :d, BcfDec,
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# :max_unpack, :int,
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# :unpacked, :int,
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# :unpack_size, [:int, 3],
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# :errcode, :int
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#
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# bit_fields :_n_info_allele,
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# :n_info, 16,
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# :n_allele, 16
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#
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# bit_fields :_n_fmt_sample,
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# :n_fmt, 8,
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# :n_sample, 24
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# end
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def bit_fields(*args)
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unless instance_variable_defined?(:@bit_fields_hash_table)
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@bit_fields_hash_table = {}
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prepend BitFieldsModule
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end
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parent = args.shift
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labels = []
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widths = []
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args.each_slice(2) do |l, w|
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labels << l
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widths << w
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end
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starts = widths.inject([0]) do |result, w|
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result << (result.last + w)
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end
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labels.zip(starts, widths).each do |l, s, w|
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@bit_fields_hash_table[l] = [parent, s, w]
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+
end
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end
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end
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end
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end
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+
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131
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require_relative "libhts/constants"
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132
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+
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133
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# alphabetical order
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require_relative "libhts/bgzf"
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require_relative "libhts/faidx"
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require_relative "libhts/hfile"
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require_relative "libhts/hts"
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require_relative "libhts/sam"
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require_relative "libhts/kfunc"
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require_relative "libhts/tbx"
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141
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require_relative "libhts/vcf"
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@@ -1,34 +1,34 @@
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1
1
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# frozen_string_literal: true
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2
2
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3
3
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module HTS
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4
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-
module
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4
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+
module LibHTS
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5
5
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typedef :pointer, :HFILE
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6
6
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typedef :int64, :hts_pos_t
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7
7
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typedef :pointer, :bam_plp_auto_f
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8
8
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9
9
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# kstring
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10
10
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11
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-
class KString <
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+
class KString < FFI::Struct
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12
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layout \
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13
13
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:l, :size_t,
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14
14
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:m, :size_t,
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:s, :string
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16
16
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end
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17
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18
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-
class KSeq <
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+
class KSeq < FFI::Struct
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19
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layout \
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:name, KString,
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21
21
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:comment, KString,
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22
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:seq, KString,
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23
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:qual, KString,
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24
24
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:last_char, :int,
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25
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-
:f, :pointer #
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+
:f, :pointer # kstream_t
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26
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end
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27
27
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28
28
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# BGZF
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29
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-
class BGZF <
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29
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+
class BGZF < FFI::BitStruct
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30
30
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layout \
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31
|
-
:
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31
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+
:_flags, :uint, # bit_fields
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32
32
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:cache_size, :int,
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33
33
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:block_length, :int,
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34
34
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:block_clength, :int,
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@@ -44,9 +44,29 @@ module HTS
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44
44
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:idx_build_otf, :int,
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45
45
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:gz_stream, :pointer,
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46
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:seeked, :int64
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47
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+
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48
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+
bit_fields :_flags,
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49
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+
:errcode, 16,
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50
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+
:_reserved, 1,
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51
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+
:is_write, 1,
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52
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+
:no_eof_block, 1,
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53
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+
:is_be, 1,
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54
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+
:compress_level, 9,
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55
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+
:last_block_eof, 1,
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56
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+
:is_compressed, 1,
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57
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+
:is_gzip, 1
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|
47
58
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end
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48
59
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49
60
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# hts
|
|
61
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+
HtsLogLevel = enum(
|
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62
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+
:off, # All logging disabled.
|
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63
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+
:error, # Logging of errors only.
|
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64
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+
:warning, 3, # Logging of errors and warnings.
|
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65
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+
:info, # Logging of errors, warnings, and normal but significant events.
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66
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+
:debug, # Logging of all except the most detailed debug events.
|
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67
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+
:trace # All logging enabled.
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68
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+
)
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69
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+
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50
70
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HtsFormatCategory = enum(
|
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51
71
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:unknown_category,
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52
72
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:sequence_data, # Sequence data -- SAM, BAM, CRAM, etc
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@@ -105,7 +125,7 @@ module HTS
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105
125
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:HTS_OPT_BLOCK_SIZE
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106
126
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)
|
|
107
127
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|
|
108
|
-
class HtsFormat <
|
|
128
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+
class HtsFormat < FFI::Struct
|
|
109
129
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layout \
|
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110
130
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:category, HtsFormatCategory,
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111
131
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:format, HtsExactFormat,
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@@ -119,7 +139,7 @@ module HTS
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119
139
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:specific, :pointer
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120
140
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end
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|
121
141
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|
|
122
|
-
class HtsIdx <
|
|
142
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+
class HtsIdx < FFI::Struct
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123
143
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layout \
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|
124
144
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:fmt, :int,
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125
145
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:min_shift, :int,
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@@ -152,7 +172,7 @@ module HTS
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152
172
|
end
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153
173
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|
|
154
174
|
# HtsFile
|
|
155
|
-
class SamHdr <
|
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175
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+
class SamHdr < FFI::Struct
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156
176
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layout \
|
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157
177
|
:n_targets, :int32,
|
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158
178
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:ignore_sam_err, :int32,
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@@ -168,9 +188,9 @@ module HTS
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168
188
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169
189
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BamHdr = SamHdr
|
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170
190
|
|
|
171
|
-
class HtsFile <
|
|
191
|
+
class HtsFile < FFI::BitStruct
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|
172
192
|
layout \
|
|
173
|
-
:
|
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193
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+
:_flags, :uint32, # bit_fields
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174
194
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:lineno, :int64,
|
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175
195
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:line, KString,
|
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176
196
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:fn, :string,
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@@ -186,17 +206,25 @@ module HTS
|
|
|
186
206
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:idx, HtsIdx.ptr,
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|
187
207
|
:fnidx, :string,
|
|
188
208
|
:bam_header, SamHdr.ptr
|
|
209
|
+
|
|
210
|
+
bit_fields :_flags,
|
|
211
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+
:is_bin, 1,
|
|
212
|
+
:is_write, 1,
|
|
213
|
+
:is_be, 1,
|
|
214
|
+
:is_cram, 1,
|
|
215
|
+
:is_bgzf, 1,
|
|
216
|
+
:dummy, 27
|
|
189
217
|
end
|
|
190
218
|
|
|
191
219
|
SamFile = HtsFile
|
|
192
220
|
|
|
193
|
-
class HtsThreadPool <
|
|
221
|
+
class HtsThreadPool < FFI::Struct
|
|
194
222
|
layout \
|
|
195
223
|
:pool, :pointer,
|
|
196
224
|
:qsize, :int
|
|
197
225
|
end
|
|
198
226
|
|
|
199
|
-
class HtsOpt <
|
|
227
|
+
class HtsOpt < FFI::Struct
|
|
200
228
|
layout \
|
|
201
229
|
:arg, :string,
|
|
202
230
|
:opt, HtsFmtOption,
|
|
@@ -208,9 +236,9 @@ module HTS
|
|
|
208
236
|
:next, HtsOpt.ptr
|
|
209
237
|
end
|
|
210
238
|
|
|
211
|
-
class HtsItr <
|
|
239
|
+
class HtsItr < FFI::BitStruct
|
|
212
240
|
layout \
|
|
213
|
-
:
|
|
241
|
+
:_flags, :uint32, # bit_fields
|
|
214
242
|
:tid, :int,
|
|
215
243
|
:n_off, :int,
|
|
216
244
|
:i, :int,
|
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@@ -235,9 +263,17 @@ module HTS
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235
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:m, :int,
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236
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:a, :pointer
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237
265
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)
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266
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+
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267
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+
bit_fields :_flags,
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268
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+
:read_rest, 1,
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269
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+
:finished, 1,
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270
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+
:is_cram, 1,
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271
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+
:nocoor, 1,
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272
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:multi, 1,
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273
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+
:dummy, 27
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end
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239
275
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240
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-
class Bam1Core <
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276
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+
class Bam1Core < FFI::Struct
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layout \
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:pos, :hts_pos_t,
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279
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:tid, :int32,
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@@ -253,23 +289,50 @@ module HTS
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:isize, :hts_pos_t
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end
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291
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256
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-
class Bam1 <
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292
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+
class Bam1 < FFI::Struct
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layout \
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:core, Bam1Core,
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:id, :uint64,
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:data, :pointer, # uint8_t
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:l_data, :int,
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:m_data, :uint32,
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263
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-
:
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+
:_mempolicy, :uint32 # bit_fields
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300
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+
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301
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+
# bit_fields :_mempolicy,
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# :mempolicy, 2,
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# :_reserved, 30
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end
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-
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306
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+
typedef :pointer, :bam_plp
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typedef :pointer, :bam_mplp
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308
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+
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309
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+
class BamPileupCd < FFI::Union
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310
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layout \
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:p, :pointer,
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:i, :int64_t,
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:f, :double
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end
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class
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+
class BamPileup1 < FFI::BitStruct
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layout \
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318
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:b, Bam1.ptr,
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:qpos, :int32_t,
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:indel, :int,
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:level, :int,
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:_flags, :uint32_t, # bit_fields
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:cd, BamPileupCd,
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:cigar_ind, :int
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bit_fields :_flags,
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:is_del, 1,
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:is_head, 1,
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:is_tail, 1,
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:is_refskip, 1,
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:_reserved, 1,
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:aux, 27
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end
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-
class TbxConf <
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+
class TbxConf < FFI::Struct
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layout \
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:preset, :int32,
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:sc, :int32,
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@@ -279,7 +342,7 @@ module HTS
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:line_skip, :int32
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end
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class Tbx <
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+
class Tbx < FFI::Struct
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layout \
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:conf, TbxConf.ptr,
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:idx, HtsIdx.ptr,
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@@ -290,7 +353,7 @@ module HTS
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FaiFormatOptions = enum(:FAI_NONE, :FAI_FASTA, :FAI_FASTQ)
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class Faidx <
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class Faidx < FFI::Struct
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layout :bgzf, BGZF,
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:n, :int,
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:m, :int,
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@@ -301,13 +364,13 @@ module HTS
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# vcf
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class
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+
class BcfVariant < FFI::Struct
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layout \
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:type, :int,
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:n, :int
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end
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-
class BcfHrec <
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+
class BcfHrec < FFI::Struct
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layout \
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:type, :int,
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:key, :string,
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@@ -317,7 +380,7 @@ module HTS
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:vals, :pointer
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end
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class BcfFmt <
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class BcfFmt < FFI::BitStruct
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layout \
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:id, :int,
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:n, :int,
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@@ -325,10 +388,14 @@ module HTS
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:type, :int,
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:p, :pointer, # uint8_t
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:p_len, :uint32,
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-
:
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+
:_p_off_free, :uint32 # bit_fields
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+
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bit_fields :_p_off_free,
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:p_off, 31,
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:p_free, 1
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end
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class BcfInfo <
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+
class BcfInfo < FFI::BitStruct
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layout \
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:key, :int,
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:type, :int,
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@@ -339,24 +406,28 @@ module HTS
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),
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:vptr, :pointer,
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:vptr_len, :uint32,
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342
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-
:
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+
:_vptr_off_free, :uint32, # bit_fields
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:len, :int
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+
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+
bit_fields :_vptr_off_free,
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:vptr_off, 31,
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+
:vptr_free, 1
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end
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346
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-
class BcfIdinfo <
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+
class BcfIdinfo < FFI::Struct
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layout \
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348
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:info, [:uint8, 3],
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:hrec, [BcfHrec.ptr, 3],
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:id, :int
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end
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353
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-
class BcfIdpair <
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+
class BcfIdpair < FFI::Struct
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layout \
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355
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:key, :string,
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356
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:val, BcfIdinfo.ptr
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end
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358
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359
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-
class BcfHdr <
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+
class BcfHdr < FFI::Struct
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layout \
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:n, [:int, 3],
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:id, [BcfIdpair.ptr, 3],
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@@ -373,7 +444,7 @@ module HTS
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:m, [:int, 3]
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end
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375
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376
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-
class BcfDec <
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447
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+
class BcfDec < FFI::Struct
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layout \
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:m_fmt, :int,
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379
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:m_info, :int,
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@@ -388,21 +459,21 @@ module HTS
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:allele, :pointer,
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:info, BcfInfo.ptr,
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:fmt, BcfFmt.ptr,
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-
:var,
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+
:var, BcfVariant.ptr,
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:n_var, :int,
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:var_type, :int,
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:shared_dirty, :int,
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:indiv_dirty, :int
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396
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end
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397
468
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398
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-
class Bcf1 <
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469
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+
class Bcf1 < FFI::BitStruct
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399
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layout \
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400
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:pos, :hts_pos_t,
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401
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:rlen, :hts_pos_t,
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:rid, :int32_t,
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403
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:qual, :float,
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404
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-
:
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405
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-
:
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475
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+
:_n_info_allele, :uint32_t,
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+
:_n_fmt_sample, :uint32_t,
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406
477
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:shared, KString,
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407
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:indiv, KString,
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408
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:d, BcfDec,
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@@ -411,13 +482,13 @@ module HTS
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:unpack_size, [:int, 3],
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:errcode, :int
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413
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414
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-
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415
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-
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416
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-
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485
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+
bit_fields :_n_info_allele,
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486
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+
:n_info, 16,
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487
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+
:n_allele, 16
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417
488
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418
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-
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419
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-
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420
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-
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489
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+
bit_fields :_n_fmt_sample,
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490
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+
:n_fmt, 8,
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491
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+
:n_sample, 24
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421
492
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end
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422
493
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end
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494
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end
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