htslib 0.0.2 → 0.0.3
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- 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/ffi.rb
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# frozen_string_literal: true
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module HTS
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module FFI
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extend ::FFI::Library
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begin
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ffi_lib HTS.ffi_lib
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rescue LoadError => e
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raise LoadError, "#{e}\nCould not find #{HTS.ffi_lib}"
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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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def union_layout(*args)
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Class.new(FFI::Union) { layout(*args) }
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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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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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def bitfields(*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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require_relative 'ffi/constants'
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# alphabetical order
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require_relative 'ffi/bgzf'
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require_relative 'ffi/faidx'
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require_relative 'ffi/hfile'
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require_relative 'ffi/hts'
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require_relative 'ffi/sam'
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require_relative 'ffi/kfunc'
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require_relative 'ffi/tbx'
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require_relative 'ffi/vcf'
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