Class: Minibwa::Hit

Inherits:
Object
  • Object
show all
Defined in:
lib/minibwa/hit.rb,
ext/minibwa/mb_hit.c

Overview

A single alignment of one query against the reference.

The fields are filled in by mb_hit.c. This file reopens the class for the values that can be derived without touching C: CIGAR formatting, the soft-clipped CIGAR rebuilt from qs/qe -- upstream only reports the aligned region -- the strand character, and #inspect.

Constant Summary collapse

CIGAR_STR =

CIGAR operation characters indexed by operation code.

'MIDNSHP=XB'

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#blen ⇒ Integer (readonly)

Returns alignment block length.

Returns:

  • (Integer) —

    alignment block length.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#cigar ⇒ Array<Array(Integer, Integer)> (readonly)

Returns CIGAR operations as [length, op] pairs.

Returns:

  • (Array<Array(Integer, Integer)>) —

    CIGAR operations as [length, op] pairs.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#cnt ⇒ Integer (readonly)

Returns number of seed hits.

Returns:

  • (Integer) —

    number of seed hits.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#cs_flag ⇒ Integer (readonly)

Returns CS tag flags.

Returns:

  • (Integer) —

    CS tag flags.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#ctg ⇒ String? (readonly)

Returns target contig name, when available.

Returns:

  • (String, nil) —

    target contig name, when available.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#dp_max ⇒ Integer (readonly)

Returns dynamic-programming maximum.

Returns:

  • (Integer) —

    dynamic-programming maximum.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#dp_max0 ⇒ Integer (readonly)

Returns first dynamic-programming maximum.

Returns:

  • (Integer) —

    first dynamic-programming maximum.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#dp_max2 ⇒ Integer (readonly)

Returns second dynamic-programming maximum.

Returns:

  • (Integer) —

    second dynamic-programming maximum.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#dp_score ⇒ Integer (readonly)

Returns dynamic-programming score.

Returns:

  • (Integer) —

    dynamic-programming score.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#flt ⇒ Boolean (readonly)

Returns whether the hit is filtered.

Returns:

  • (Boolean) —

    whether the hit is filtered.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#frac_high ⇒ Boolean (readonly)

Returns whether the high-frequency seed fraction is high.

Returns:

  • (Boolean) —

    whether the high-frequency seed fraction is high.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#hash ⇒ Integer (readonly)

Returns upstream hash value for tie-breaking.

Returns:

  • (Integer) —

    upstream hash value for tie-breaking.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#inv ⇒ Boolean (readonly)

Returns whether the hit represents an inversion.

Returns:

  • (Boolean) —

    whether the hit represents an inversion.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#mapq ⇒ Integer (readonly)

Returns mapping quality.

Returns:

  • (Integer) —

    mapping quality.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#mlen ⇒ Integer (readonly)

Returns number of matching bases.

Returns:

  • (Integer) —

    number of matching bases.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#n_ambi ⇒ Integer (readonly)

Returns number of ambiguous reference bases.

Returns:

  • (Integer) —

    number of ambiguous reference bases.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#n_sub ⇒ Integer (readonly)

Returns number of suboptimal hits.

Returns:

  • (Integer) —

    number of suboptimal hits.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#proper_pair ⇒ Boolean (readonly)

Returns whether the hit is part of a proper pair.

Returns:

  • (Boolean) —

    whether the hit is part of a proper pair.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#qe ⇒ Integer (readonly)

Returns zero-based query end.

Returns:

  • (Integer) —

    zero-based query end.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#qs ⇒ Integer (readonly)

Returns zero-based query start.

Returns:

  • (Integer) —

    zero-based query start.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#rescued ⇒ Boolean (readonly)

Returns whether paired-end rescue found the hit.

Returns:

  • (Boolean) —

    whether paired-end rescue found the hit.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#rev ⇒ Boolean (readonly)

Returns whether the hit is on the reverse strand.

Returns:

  • (Boolean) —

    whether the hit is on the reverse strand.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#sam_pri ⇒ Boolean (readonly)

Returns whether the hit is primary in SAM output.

Returns:

  • (Boolean) —

    whether the hit is primary in SAM output.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#score ⇒ Integer (readonly)

Returns alignment score.

Returns:

  • (Integer) —

    alignment score.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#score0 ⇒ Integer (readonly)

Returns best-chain score before post-processing.

Returns:

  • (Integer) —

    best-chain score before post-processing.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#seed_ratio ⇒ Boolean (readonly)

Returns whether the seed ratio flag is set.

Returns:

  • (Boolean) —

    whether the seed ratio flag is set.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#split ⇒ Boolean (readonly)

Returns whether the hit is split.

Returns:

  • (Boolean) —

    whether the hit is split.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#split_inv ⇒ Boolean (readonly)

Returns whether the split hit is inverted.

Returns:

  • (Boolean) —

    whether the split hit is inverted.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#subsc ⇒ Integer (readonly)

Returns suboptimal alignment score.

Returns:

  • (Integer) —

    suboptimal alignment score.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#te ⇒ Integer (readonly)

Returns zero-based target end.

Returns:

  • (Integer) —

    zero-based target end.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#tid ⇒ Object (readonly)

attr_readers for all fields



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

#ts ⇒ Integer (readonly)

Returns zero-based target start.

Returns:

  • (Integer) —

    zero-based target start.



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# File 'lib/minibwa/hit.rb', line 75

class Hit
  # CIGAR operation characters indexed by operation code.
  CIGAR_STR = 'MIDNSHP=XB'

  # Returns the CIGAR string for the aligned region (no soft/hard clips).
  def cigar_str
    @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
  end

  # Returns the full CIGAR string including soft clips.
  #
  # The query length is required because the Hit only stores the aligned
  # region (qs/qe); the clips are derived from the difference.
  #
  #   hit.full_cigar_str(query.length)  # => "2S35M3S"
  def full_cigar_str(query_len)
    Sam.build_full_cigar(self, query_len)
  end

  # Returns the strand as '+' or '-'.
  def strand
    rev ? '-' : '+'
  end

  # Returns the target (reference) span length.
  def tlen
    te - ts
  end

  # Returns a compact representation of the most commonly inspected fields.
  def inspect
    attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
    "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
  end
end

Instance Method Details

#cigar_str ⇒ Object

Returns the CIGAR string for the aligned region (no soft/hard clips).



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# File 'lib/minibwa/hit.rb', line 80

def cigar_str
  @cigar.map { |len, op| "#{len}#{CIGAR_STR[op]}" }.join
end

#full_cigar_str(query_len) ⇒ Object

Returns the full CIGAR string including soft clips.

The query length is required because the Hit only stores the aligned region (qs/qe); the clips are derived from the difference.

hit.full_cigar_str(query.length)  # => "2S35M3S"


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# File 'lib/minibwa/hit.rb', line 90

def full_cigar_str(query_len)
  Sam.build_full_cigar(self, query_len)
end

#inspect ⇒ Object

Returns a compact representation of the most commonly inspected fields.



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# File 'lib/minibwa/hit.rb', line 105

def inspect
  attrs = %i[tid ctg ts te qs qe strand score mapq mlen blen]
  "#<#{self.class.name} #{attrs.map { |a| "#{a}=#{send(a).inspect}" }.join(' ')}>"
end

#strand ⇒ Object

Returns the strand as '+' or '-'.



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# File 'lib/minibwa/hit.rb', line 95

def strand
  rev ? '-' : '+'
end

#tlen ⇒ Object

Returns the target (reference) span length.



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# File 'lib/minibwa/hit.rb', line 100

def tlen
  te - ts
end