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. For more genomics resource definitions, see Fundamentals of Google Genomics

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



1773
1774
1775
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1773

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>) 


1652
1653
1654
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1652

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) 


1663
1664
1665
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1663

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:



1669
1670
1671
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1669

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) 


1674
1675
1676
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1674

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) 


1681
1682
1683
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1681

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) 


1687
1688
1689
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1687

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) 


1692
1693
1694
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1692

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) 


1698
1699
1700
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1698

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>>) 


1704
1705
1706
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1704

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:



1712
1713
1714
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1712

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) 


1717
1718
1719
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1717

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) 


1723
1724
1725
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1723

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) 


1732
1733
1734
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1732

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) 


1738
1739
1740
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1738

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) 


1744
1745
1746
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1744

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) 


1754
1755
1756
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1754

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) 


1770
1771
1772
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1770

def supplementary_alignment
  @supplementary_alignment
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
1791
1792
1793
1794
1795
1796
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 1778

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