Primary change is to generate_sysdata.R. Previous code was overly restrictive in that it removed any individual ID who has any entry at all for mom, dad, siblings, children, 2d, 3d, even if those individuals weren't in the sequencing data. Now we compile a list of relatives - unique IDs listed in any of the momid, dadid, siblings, children, 2d, 3d fields, and then remove any individuals who are one of these relatives with sequencing data. This only removes two individuals.
Moves text file list from data-raw (not built) to inst/extdata so that these text files for bcftools view are available anywhere skater is installed.
Fixes #22 cc @genignored
relatives- unique IDs listed in any of the momid, dadid, siblings, children, 2d, 3d fields, and then remove any individuals who are one of these relatives with sequencing data. This only removes two individuals.data-raw(not built) toinst/extdataso that these text files forbcftools vieware available anywhere skater is installed.