Class: Google::Apis::GenomicsV1::Read

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 read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set.

Reverse-stranded reads

Mapped reads (reads having a non-null alignment) can be aligned to either the forward or the reverse strand of their associated reference. Strandedness of a mapped read is encoded by alignment.position.reverseStrand. If we consider the reference to be a forward-stranded coordinate space of [0, reference.length) with 0 as the left-most position and reference.length as the right-most position, reads are always aligned left to right. That is, alignment.position.position always refers to the left-most reference coordinate and alignment.cigar describes the alignment of this read to the reference from left to right. All per-base fields such as alignedSequence and alignedQuality share this same left-to-right orientation; this is true of reads which are aligned to either strand. For reverse-stranded reads, this means that alignedSequence is the reverse complement of the bases that were originally reported by the sequencing machine.

Generating a reference-aligned sequence string

When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this: out = "" offset = 0 for c in read.alignment.cigar switch c.operation case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.operationLength) break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD": break return out

Converting to SAM's CIGAR string

The following pseudocode generates a SAM CIGAR string from the cigar field. Note that this is a lossy conversion (cigar.referenceSequence is lost). cigarMap = "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH": "X", cigarStr = "" for c in read.alignment.cigar cigarStr += c.operationLength + cigarMap[c.operation] return cigarStr

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) ⇒ Read

Returns a new instance of Read



1979
1980
1981
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1979

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

Instance Attribute Details

#aligned_quality ⇒ Array<Fixnum>

The quality of the read sequence contained in this alignment record (equivalent to QUAL in SAM). alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence. Corresponds to the JSON property alignedQuality

Returns:

  • (Array<Fixnum>) 


1858
1859
1860
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1858

def aligned_quality
  @aligned_quality
end

#aligned_sequence ⇒ String

The bases of the read sequence contained in this alignment record, without CIGAR operations applied (equivalent to SEQ in SAM). alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence. Corresponds to the JSON property alignedSequence

Returns:

  • (String) 


1869
1870
1871
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1869

def aligned_sequence
  @aligned_sequence
end

#alignment ⇒ Google::Apis::GenomicsV1::LinearAlignment

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

Returns:



1875
1876
1877
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1875

def alignment
  @alignment
end

#duplicate_fragment ⇒ Boolean Also known as: duplicate_fragment?

The fragment is a PCR or optical duplicate (SAM flag 0x400). Corresponds to the JSON property duplicateFragment

Returns:

  • (Boolean) 


1880
1881
1882
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1880

def duplicate_fragment
  @duplicate_fragment
end

#failed_vendor_quality_checks ⇒ Boolean Also known as: failed_vendor_quality_checks?

Whether this read did not pass filters, such as platform or vendor quality controls (SAM flag 0x200). Corresponds to the JSON property failedVendorQualityChecks

Returns:

  • (Boolean) 


1887
1888
1889
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1887

def failed_vendor_quality_checks
  @failed_vendor_quality_checks
end

#fragment_length ⇒ Fixnum

The observed length of the fragment, equivalent to TLEN in SAM. Corresponds to the JSON property fragmentLength

Returns:

  • (Fixnum) 


1893
1894
1895
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1893

def fragment_length
  @fragment_length
end

#fragment_name ⇒ String

The fragment name. Equivalent to QNAME (query template name) in SAM. Corresponds to the JSON property fragmentName

Returns:

  • (String) 


1898
1899
1900
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1898

def fragment_name
  @fragment_name
end

#id ⇒ String

The server-generated read ID, unique across all reads. This is different from the fragmentName. Corresponds to the JSON property id

Returns:

  • (String) 


1904
1905
1906
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1904

def id
  @id
end

#info ⇒ Hash<String,Array<Object>>

A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values). Corresponds to the JSON property info

Returns:

  • (Hash<String,Array<Object>>) 


1910
1911
1912
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1910

def info
  @info
end

#next_mate_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 nextMatePosition

Returns:



1918
1919
1920
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1918

def next_mate_position
  @next_mate_position
end

#number_reads ⇒ Fixnum

The number of reads in the fragment (extension to SAM flag 0x1). Corresponds to the JSON property numberReads

Returns:

  • (Fixnum) 


1923
1924
1925
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1923

def number_reads
  @number_reads
end

#proper_placement ⇒ Boolean Also known as: proper_placement?

The orientation and the distance between reads from the fragment are consistent with the sequencing protocol (SAM flag 0x2). Corresponds to the JSON property properPlacement

Returns:

  • (Boolean) 


1929
1930
1931
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1929

def proper_placement
  @proper_placement
end

#read_group_id ⇒ String

The ID of the read group this read belongs to. A read belongs to exactly one read group. This is a server-generated ID which is distinct from SAM's RG tag (for that value, see ReadGroup.name). Corresponds to the JSON property readGroupId

Returns:

  • (String) 


1938
1939
1940
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1938

def read_group_id
  @read_group_id
end

#read_group_set_id ⇒ String

The ID of the read group set this read belongs to. A read belongs to exactly one read group set. Corresponds to the JSON property readGroupSetId

Returns:

  • (String) 


1944
1945
1946
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1944

def read_group_set_id
  @read_group_set_id
end

#read_number ⇒ Fixnum

The read number in sequencing. 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80. Corresponds to the JSON property readNumber

Returns:

  • (Fixnum) 


1950
1951
1952
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1950

def read_number
  @read_number
end

#secondary_alignment ⇒ Boolean Also known as: secondary_alignment?

Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary alignment represents an alternative to the primary alignment for this read. Aligners may return secondary alignments if a read can map ambiguously to multiple coordinates in the genome. By convention, each read has one and only one alignment where both secondaryAlignment and supplementaryAlignment are false. Corresponds to the JSON property secondaryAlignment

Returns:

  • (Boolean) 


1960
1961
1962
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1960

def secondary_alignment
  @secondary_alignment
end

#supplementary_alignment ⇒ Boolean Also known as: supplementary_alignment?

Whether this alignment is supplementary. Equivalent to SAM flag 0x800. Supplementary alignments are used in the representation of a chimeric alignment. In a chimeric alignment, a read is split into multiple linear alignments that map to different reference contigs. The first linear alignment in the read will be designated as the representative alignment; the remaining linear alignments will be designated as supplementary alignments. These alignments may have different mapping quality scores. In each linear alignment in a chimeric alignment, the read will be hard clipped. The alignedSequence and alignedQuality fields in the alignment record will only represent the bases for its respective linear alignment. Corresponds to the JSON property supplementaryAlignment

Returns:

  • (Boolean) 


1976
1977
1978
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1976

def supplementary_alignment
  @supplementary_alignment
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1984

def update!(**args)
  @aligned_quality = args[:aligned_quality] if args.key?(:aligned_quality)
  @aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence)
  @alignment = args[:alignment] if args.key?(:alignment)
  @duplicate_fragment = args[:duplicate_fragment] if args.key?(:duplicate_fragment)
  @failed_vendor_quality_checks = args[:failed_vendor_quality_checks] if args.key?(:failed_vendor_quality_checks)
  @fragment_length = args[:fragment_length] if args.key?(:fragment_length)
  @fragment_name = args[:fragment_name] if args.key?(:fragment_name)
  @id = args[:id] if args.key?(:id)
  @info = args[:info] if args.key?(:info)
  @next_mate_position = args[:next_mate_position] if args.key?(:next_mate_position)
  @number_reads = args[:number_reads] if args.key?(:number_reads)
  @proper_placement = args[:proper_placement] if args.key?(:proper_placement)
  @read_group_id = args[:read_group_id] if args.key?(:read_group_id)
  @read_group_set_id = args[:read_group_set_id] if args.key?(:read_group_set_id)
  @read_number = args[:read_number] if args.key?(:read_number)
  @secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment)
  @supplementary_alignment = args[:supplementary_alignment] if args.key?(:supplementary_alignment)
end