Parse a data frame with primer information

Parse a data frame with primer information

Usage

parse_primer_tab(primer_tab, amplicons = NULL)

Arguments

primer_tab

Primer table (data frame-like; see details)

amplicons

Character vector of amplicons pooled in the library; their names should be in the form forward-reverse (primer names should not contain dashes)

Value

a named list of amplicon metadata (named by amplicons = forward-reverse). Each amplicon-specific item is another list with two entries (for forward and reverse), which are again lists with following entries:

• primer: named vector of primer sequences

• index: named vector of index sequences

• index_len: the length of the index sequences (no variable length currently allowed, but lengths may vary between forward and reverse sample indexes)

Details

Columns of primer_tab:

• primer-index: Primer name and sample index name, delimited by a dash; the primer names must not contain dashes and both primer and index should correspond to the names in the amplicon column of the sample table (see parse_sample_tab).

• index_seq sample index sequence

• primer_seq primer sequence (repeated)

If amplicon is not provided, the forward/reverse primers are assumed to be in order. amplicon may be obtained from the amplicon column of the sample table (see parse_sample_tab).