Class: HTS::Bam::BaseMod::Modification

Inherits:
Object
  • Object
show all
Defined in:
lib/hts/bam/base_mod.rb

Overview

Individual base modification information

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(modified_base:, canonical_base:, strand:, qual:) ⇒ Modification

Returns a new instance of Modification.

Parameters:

  • modified_base (Integer) —

    Modification code as char or -ChEBI

  • canonical_base (Integer) —

    Canonical base (A, C, G, T, N)

  • strand (Integer) —

    0 or 1 for +/- strand

  • qual (Integer) —

    Quality (256*probability) or -1 if unknown



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# File 'lib/hts/bam/base_mod.rb', line 27

def initialize(modified_base:, canonical_base:, strand:, qual:)
  @modified_base = modified_base
  @canonical_base = canonical_base
  @strand = strand
  @qual = qual
end

Instance Attribute Details

#canonical_base ⇒ Object (readonly)

Returns the value of attribute canonical_base.



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# File 'lib/hts/bam/base_mod.rb', line 21

def canonical_base
  @canonical_base
end

#modified_base ⇒ Object (readonly)

Returns the value of attribute modified_base.



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# File 'lib/hts/bam/base_mod.rb', line 21

def modified_base
  @modified_base
end

#qual ⇒ Object (readonly)

Returns the value of attribute qual.



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# File 'lib/hts/bam/base_mod.rb', line 21

def qual
  @qual
end

#strand ⇒ Object (readonly)

Returns the value of attribute strand.



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# File 'lib/hts/bam/base_mod.rb', line 21

def strand
  @strand
end

Instance Method Details

#canonical ⇒ String

Get canonical base as character

Returns:

  • (String) —

    Single character (A, C, G, T, N)



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# File 'lib/hts/bam/base_mod.rb', line 42

def canonical
  @canonical_base.chr
end

#code ⇒ String

Get modification code as character or ChEBI number as string

Returns:

  • (String) —

    Single character code or ChEBI number as string



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# File 'lib/hts/bam/base_mod.rb', line 36

def code
  @modified_base > 0 ? @modified_base.chr : @modified_base.to_s
end

#inspect ⇒ String

Inspect string

Returns:

  • (String) —

    Inspect string



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# File 'lib/hts/bam/base_mod.rb', line 80

def inspect
  "#<HTS::Bam::BaseMod::Modification #{self}>"
end

#probability ⇒ Float?

Get likelihood as a probability (0.0-1.0)

Returns:

  • (Float, nil) —

    Probability or nil if qual is -1



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# File 'lib/hts/bam/base_mod.rb', line 48

def probability
  return nil if @qual == -1

  @qual / 256.0
end

#to_h ⇒ Hash

Convert to hash representation

Returns:

  • (Hash) —

    Hash with modification information



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# File 'lib/hts/bam/base_mod.rb', line 56

def to_h
  {
    modified_base: @modified_base,
    code: code,
    canonical_base: @canonical_base,
    canonical: canonical,
    strand: @strand,
    qual: @qual,
    probability: probability
  }
end

#to_s ⇒ String

String representation

Returns:

  • (String) —

    String representation of the modification



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# File 'lib/hts/bam/base_mod.rb', line 70

def to_s
  if @qual >= 0
    "#{canonical}->#{code}(#{probability.round(3)})"
  else
    "#{canonical}->#{code}"
  end
end