Class: HTS::Bam::BaseMod::Position

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

Overview

Position-specific modification information

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(position, modifications) ⇒ Position

Returns a new instance of Position.

Parameters:

  • position (Integer) —

    Position in query sequence

  • modifications (Array<Modification>) —

    Array of modifications at this position



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# File 'lib/hts/bam/base_mod.rb', line 92

def initialize(position, modifications)
  @position = position
  @modifications = modifications
end

Instance Attribute Details

#modifications ⇒ Object (readonly)

Returns the value of attribute modifications.



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# File 'lib/hts/bam/base_mod.rb', line 88

def modifications
  @modifications
end

#position ⇒ Object (readonly)

Returns the value of attribute position.



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# File 'lib/hts/bam/base_mod.rb', line 88

def position
  @position
end

Instance Method Details

#hydroxymethylated? ⇒ Boolean

Check if this position has hydroxymethylation

Returns:

  • (Boolean) —

    true if any modification is hydroxymethylation ('h')



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# File 'lib/hts/bam/base_mod.rb', line 105

def hydroxymethylated?
  @modifications.any? { |m| m.code == "h" }
end

#inspect ⇒ String

Inspect string

Returns:

  • (String) —

    Inspect string



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# File 'lib/hts/bam/base_mod.rb', line 127

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

#methylated? ⇒ Boolean

Check if this position has methylation

Returns:

  • (Boolean) —

    true if any modification is methylation ('m')



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# File 'lib/hts/bam/base_mod.rb', line 99

def methylated?
  @modifications.any? { |m| m.code == "m" }
end

#to_h ⇒ Hash

Convert to hash representation

Returns:

  • (Hash) —

    Hash with position information



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# File 'lib/hts/bam/base_mod.rb', line 111

def to_h
  {
    position: @position,
    modifications: @modifications.map(&:to_h)
  }
end

#to_s ⇒ String

String representation

Returns:

  • (String) —

    String representation



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# File 'lib/hts/bam/base_mod.rb', line 120

def to_s
  mods_str = @modifications.map(&:to_s).join(", ")
  "pos=#{@position} [#{mods_str}]"
end