Extract sample SQL IDs from STACKS catalog file

Source: R/extract_catalog_sample.R

This function reads the output of STACKS cstacks tags file to generate a tibble of sample SQL ids that were used to generate the catalog.

extract_catalog_sql_ids(
  x = "06_ustacks_2_gstacks/catalog.tags.tsv.gz",
  parallel.core = parallel::detectCores() - 1
)

Arguments

x

(character, path). The path to the catalog.tags.tsv.gz file. Default: x = "catalog.tags.tsv.gz".
parallel.core

(integer) Enable parallel execution with the number of threads. Default: parallel.core = parallel::detectCores() - 1.

Value

The function returns a tibble with the SQL IDs.

References

Catchen JM, Amores A, Hohenlohe PA et al. (2011) Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences. G3, 1, 171-182.

Catchen JM, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140.

See also

cstacks run_cstacks

Examples

if (FALSE) {
ids <- stackr::extract_catalog_sql_id(x = "06_ustacks_2_gstacks/catalog.tags.tsv.gz")
}