Class: SSW::Align

Inherits:
Object
  • Object
show all
Defined in:
lib/ssw/align.rb

Overview

structure of the alignment result

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(ptr) ⇒ Align

Returns a new instance of Align.



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# File 'lib/ssw/align.rb', line 42

def initialize(ptr)
  @ptr          = ptr
  @cstruct      = align = FFI::Align.new(ptr)
  @score1       = align.score1
  @score2       = align.score2
  @ref_begin1   = align.ref_begin1
  @ref_end1     = align.ref_end1
  @read_begin1  = align.read_begin1
  @read_end1    = align.read_end1
  @ref_end2     = align.ref_end2
  @cigar_len    = align.cigarLen
  @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
  # Attributes for ruby binding only
  @cigar_string = array_to_cigar_string(@cigar)
  SSW.align_destroy(ptr)
end

Instance Attribute Details

#cigar ⇒ Array (readonly)

Returns best alignment cigar; stored the same as that in BAM format, high 28 bits: length, low 4 bits: M/I/D (0/1/2); cigar = 0 when the best alignment path is not available.

Returns:

  • (Array) —

    best alignment cigar; stored the same as that in BAM format, high 28 bits: length, low 4 bits: M/I/D (0/1/2); cigar = 0 when the best alignment path is not available



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#cigar_len ⇒ Integer

Returns length of the cigar string; cigarLen = 0 when the best alignment path is not available.

Returns:

  • (Integer) —

    length of the cigar string; cigarLen = 0 when the best alignment path is not available



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#cigar_string ⇒ String

Returns cigar string.

Returns:

  • (String) —

    cigar string



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#read_begin1 ⇒ Integer

Returns 0-based best alignment beginning position on read; read_begin1 = -1 when the best alignment beginning position is not available.

Returns:

  • (Integer) —

    0-based best alignment beginning position on read; read_begin1 = -1 when the best alignment beginning position is not available



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#read_end1 ⇒ Integer

Returns 0-based best alignment ending position on read.

Returns:

  • (Integer) —

    0-based best alignment ending position on read



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#read_end2 ⇒ Integer

Returns 0-based sub-optimal alignment ending position on read.

Returns:

  • (Integer) —

    0-based sub-optimal alignment ending position on read



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#ref_begin1 ⇒ Integer

Returns 0-based best alignment beginning position on reference; ref_begin1 = -1 when the best alignment beginning position is not available.

Returns:

  • (Integer) —

    0-based best alignment beginning position on reference; ref_begin1 = -1 when the best alignment beginning position is not available



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#ref_end1 ⇒ Integer

Returns 0-based best alignment ending position on reference.

Returns:

  • (Integer) —

    0-based best alignment ending position on reference



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#score1 ⇒ Integer

Returns the best alignment score.

Returns:

  • (Integer) —

    the best alignment score



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

#score2 ⇒ Integer

Returns sub-optimal alignment score.

Returns:

  • (Integer) —

    sub-optimal alignment score



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# File 'lib/ssw/align.rb', line 33

class Align
  def self.keys
    %i[score1 score2 ref_begin1 ref_end1
       read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
  end

  # This class is read_only
  attr_reader(*keys)

  def initialize(ptr)
    @ptr          = ptr
    @cstruct      = align = FFI::Align.new(ptr)
    @score1       = align.score1
    @score2       = align.score2
    @ref_begin1   = align.ref_begin1
    @ref_end1     = align.ref_end1
    @read_begin1  = align.read_begin1
    @read_end1    = align.read_end1
    @ref_end2     = align.ref_end2
    @cigar_len    = align.cigarLen
    @cigar        = cigar_len.positive? ? align.cigar[0, 4 * cigar_len].unpack('L*') : []
    # Attributes for ruby binding only
    @cigar_string = array_to_cigar_string(@cigar)
    SSW.align_destroy(ptr)
  end

  def to_h
    self.class.keys.map { |k| [k, __send__(k)] }.to_h
  end

  private

  def array_to_cigar_string(arr)
    cigar_string = String.new
    arr.each do |x|
      n = x >> 4
      m = x & 15
      c = m > 8 ? 'M' : 'MIDNSHP=X'[m]
      cigar_string << n.to_s << c
    end
    cigar_string
  end
end

Class Method Details

.keys ⇒ Object 



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# File 'lib/ssw/align.rb', line 34

def self.keys
  %i[score1 score2 ref_begin1 ref_end1
     read_begin1 read_end1 ref_end2 cigar cigar_len cigar_string]
end

Instance Method Details

#to_h ⇒ Object 



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# File 'lib/ssw/align.rb', line 59

def to_h
  self.class.keys.map { |k| [k, __send__(k)] }.to_h
end