Manipulating read metadata

Read fields

Reads have several fields that store metadata. Which fields are available depends on the type of input reads you provide.

Input format Fields

FASTA
(.fa, .fasta)

`seq:` `Str`	The sequence of the read.
`id:` `Str`	The read ID. Everything from `>` to the first whitespace in the description line.
`desc:` `Str`	The description line. Everything after the read ID.

FASTQ
(.fq, .fastq)

`seq:` `Str`	The sequence of the read.
`id:` `Str`	The read ID. Everything from `@` to the first whitespace in the description line.
`desc:` `Str`	The description line. Everything after the read ID.
`qual:` `Str`	The quality string.

SAM
(.sam, .bam)

`id \| qname:` `Str`	The read ID. Defaults to `'*'` if unavailable.
`flag:` `Num`	Combination of bitwise flags.
`rname:` `Str`	Name of the reference sequence to which the read is aligned. Defaults to `'*'` if unavailable or unmapped.
`pos:` `Num`	1-based leftmosed mapping position of the first CIGAR operation that consumes a reference base. Defaults to `0` if unmapped.
`mapq:` `Num`	Mapping quality.
`cigar:` `Str`	CIGAR string.
`rnext:` `Str`	Reference sequence name of the primary alignment of the next read in the template. Defaults to `'*'` if unavailable or unmapped.
`pnext:` `Num`	1-based position of the primary alignment of the next read in the template. Defaults to `0` if unavailable.
`tlen:` `Num`	Signed observed template length. Defaults to `0` if unavailable.
`seq:` `Str`	The sequence of the read.
`qual:` `Str`	The quality string.
`desc:` `Str`	The optional fields, as a single string.

Paired
(any formats)

`r1:` `Read`	The first read, from the file given as mandatory argument.
`r2:` `Read`	The second read, from the file given via the `--paired-with` optional argument.

Reverse-complementing

Reads can be reverse-complemented. For FASTA reads, this reverse-complements the sequence. For FASTQ and SAM reads, it additionally reverses the quality score, so that the bases still correctly correspond to quality score characters.

# reverse complement each read
-read.out!('reversed.fq')

Tagging

Information can be added to the description line of reads, such as a UMI or barcode, or any other data derived from processing with matchbox.

# tag each read with its length
read.tag('length={read.seq.len()}')

info	The string given to `tag` is appended to the read's `desc`, separated by a space. To change this prefix (e.g. when adding an optional field to a SAM read, which are tab-delimited), the optional argument `prefix` can be set.