Class: HTS::Faidx::Sequence

Inherits:
Object
  • Object
show all
Defined in:
lib/hts/faidx/sequence.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(faidx, name) ⇒ Sequence

Returns a new instance of Sequence.

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# File 'lib/hts/faidx/sequence.rb', line 6

def initialize(faidx, name)
  raise unless faidx.has_key?(name)

  @faidx = faidx
  @name = name
end

Instance Attribute Details

#faidx ⇒ Object (readonly)

Returns the value of attribute faidx.


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# File 'lib/hts/faidx/sequence.rb', line 4

def faidx
  @faidx
end

#name ⇒ Object (readonly)

Returns the value of attribute name.


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# File 'lib/hts/faidx/sequence.rb', line 4

def name
  @name
end

Instance Method Details

#[](arg) ⇒ Object

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# File 'lib/hts/faidx/sequence.rb', line 26

def [](arg)
  case arg
  when Integer
    if arg >= 0
      start = arg
      stop = arg
    else
      start = length + arg
      stop = length + arg
    end
  when Range
    arg = Range.new(arg.begin, arg.end + length, arg.exclude_end?) if arg.end&.<(0)
    arg = Range.new(arg.begin + length, arg.end, arg.exclude_end?) if arg.begin&.<(0)
    if arg.begin.nil?
      if arg.end.nil?
        start = nil
        stop = nil
      else
        start = 0
        stop = arg.exclude_end? ? arg.end - 1 : arg.end
      end
    elsif arg.end.nil?
      # always include the first base
      start = arg.begin
      stop = length - 1
    else
      start = arg.begin
      stop = arg.exclude_end? ? arg.end - 1 : arg.end
    end
  else
    raise ArgumentError
  end
  seq(start, stop)
end

#length ⇒ Object Also known as: size

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# File 'lib/hts/faidx/sequence.rb', line 13

def length
  faidx.seq_len(name)
end

#qual(start = nil, stop = nil) ⇒ Object

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# File 'lib/hts/faidx/sequence.rb', line 22

def qual(start = nil, stop = nil)
  faidx.qual(name, start, stop)
end

#seq(start = nil, stop = nil) ⇒ Object

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# File 'lib/hts/faidx/sequence.rb', line 18

def seq(start = nil, stop = nil)
  faidx.seq(name, start, stop)
end