Class: Google::Apis::GenomicsV1beta2::LinearAlignment

Inherits:
Object
  • Object
show all
Includes:
Core::Hashable
Defined in:
generated/google/apis/genomics_v1beta2/classes.rb,
generated/google/apis/genomics_v1beta2/representations.rb,
generated/google/apis/genomics_v1beta2/representations.rb

Overview

A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ LinearAlignment

Returns a new instance of LinearAlignment.


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 1189

def initialize(**args)
   update!(**args)
end

Instance Attribute Details

#cigarArray<Google::Apis::GenomicsV1beta2::CigarUnit>

Represents the local alignment of this sequence (alignment matches, indels, etc) against the reference. Corresponds to the JSON property cigar


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 1173

def cigar
  @cigar
end

#mapping_qualityFixnum

The mapping quality of this alignment. Represents how likely the read maps to this position as opposed to other locations. Corresponds to the JSON property mappingQuality

Returns:

  • (Fixnum)

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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 1179

def mapping_quality
  @mapping_quality
end

#positionGoogle::Apis::GenomicsV1beta2::Position

An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand. Corresponds to the JSON property position


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 1187

def position
  @position
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 1194

def update!(**args)
  @cigar = args[:cigar] unless args[:cigar].nil?
  @mapping_quality = args[:mapping_quality] unless args[:mapping_quality].nil?
  @position = args[:position] unless args[:position].nil?
end