extract_catalog_sql_ids: Extract sample SQL IDs from STACKS catalog file

In thierrygosselin/stackr: Run stacks pipeline for RADseq analysis inside R

Extract sample SQL IDs from STACKS catalog file

Description

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.

Usage

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

## Not run: 
ids <- stackr::extract_catalog_sql_id(x = "06_ustacks_2_gstacks/catalog.tags.tsv.gz")

## End(Not run)

thierrygosselin/stackr documentation built on April 13, 2025, 10:28 a.m.