Spot Check Read Pairing

SpotCheckReadPairing #

Confirms for every sample_strideth read ‘pair’ that the names share the same prefix (part before ‘readname_end_char’).

[[step]]
    action = "SpotCheckReadPairing"
    sample_stride = 1000 # Every nth fragment, default 1000. Must be > 0. 
    readname_end_char = '/' # u8/byte-char, Defaults to no character, meaning the entire name is compared.

When no separator character is provided the entire name must match exactly across all segments.

Otherwise the read names are truncated after the first readname_end_char, and the prefixes must match exactly. For example, use readname_end_char = “_” for typical Illumina _1/_2 suffixes.

Note that this validation requires at least two input segments so there is a name to compare against, mbf-fastq-processor will return an error otherwise.

(Closely related in concept to ValidateName).

Automatic SpotCheckReadPairing #

This step is injected automatically after your transformations when

  • more than one input segment is defined
  • and options.spot_check_read_pairing is set to true (the default)
  • and and no explicit SpotCheckReadPairing or ValidateName step is present.

See the input section for details.