Read class

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

Constructors

Read()
Read.fromJson(Map _json)

Properties

alignedQuality ↔ List<int>
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.
read / write
alignedSequence ↔ 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.
read / write
alignment LinearAlignment
The linear alignment for this alignment record. This field is null for unmapped reads.
read / write
duplicateFragment ↔ bool
The fragment is a PCR or optical duplicate (SAM flag 0x400).
read / write
failedVendorQualityChecks ↔ bool
Whether this read did not pass filters, such as platform or vendor quality controls (SAM flag 0x200).
read / write
fragmentLength ↔ int
The observed length of the fragment, equivalent to TLEN in SAM.
read / write
fragmentName ↔ String
The fragment name. Equivalent to QNAME (query template name) in SAM.
read / write
id ↔ String
The server-generated read ID, unique across all reads. This is different from the fragmentName.
read / write
info ↔ Map<String, List<Object>>
A map of additional read alignment information. This must be of the form map<string, string[]> (string key mapping to a list of string values). [...]
read / write
nextMatePosition Position
The mapping of the primary alignment of the (readNumber+1)%numberReads read in the fragment. It replaces mate position and mate strand in SAM.
read / write
numberReads ↔ int
The number of reads in the fragment (extension to SAM flag 0x1).
read / write
properPlacement ↔ bool
The orientation and the distance between reads from the fragment are consistent with the sequencing protocol (SAM flag 0x2).
read / write
readGroupId ↔ 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).
read / write
readGroupSetId ↔ String
The ID of the read group set this read belongs to. A read belongs to exactly one read group set.
read / write
readNumber ↔ int
The read number in sequencing. 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80.
read / write
secondaryAlignment ↔ bool
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.
read / write
supplementaryAlignment ↔ bool
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.
read / write
hashCode → int
The hash code for this object.
read-only, inherited
runtimeType → Type
A representation of the runtime type of the object.
read-only, inherited

Methods

toJson() → Map<String, Object>
noSuchMethod(Invocation invocation) → dynamic
Invoked when a non-existent method or property is accessed.
inherited
toString() → String
Returns a string representation of this object.
inherited

Operators

operator ==(dynamic other) → bool
The equality operator.
inherited