Class: Google::Apis::GenomicsV1::LinearAlignment

Inherits:
Object
  • Object
show all
Includes:
Core::Hashable, Core::JsonObjectSupport
Defined in:
generated/google/apis/genomics_v1/classes.rb,
generated/google/apis/genomics_v1/representations.rb,
generated/google/apis/genomics_v1/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::JsonObjectSupport

#to_json

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ LinearAlignment

Returns a new instance of LinearAlignment



559
560
561
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 559

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

Instance Attribute Details

#cigar ⇒ Array<Google::Apis::GenomicsV1::CigarUnit>

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

Returns:



549
550
551
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 549

def cigar
  @cigar
end

#mapping_quality ⇒ Fixnum

The mapping quality of this alignment. Represents how likely the read maps to this position as opposed to other locations. Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to the nearest integer. Corresponds to the JSON property mappingQuality

Returns:

  • (Fixnum) 


557
558
559
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 557

def mapping_quality
  @mapping_quality
end

#position ⇒ Google::Apis::GenomicsV1::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

Returns:



543
544
545
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 543

def position
  @position
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



564
565
566
567
568
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 564

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