file
the name of the ".sync" file where the data should be read from. Sync
files are specified in Kofler et al. (2011). Sync files contain 3 + n columns with;
col 1: chromosome (reference contig), col 2: position (in the reference contig),
col 3: reference allele, col >3: sync entries for allele frequencies for all populations
in the form A-count:T-count:C-count:G-count:N-count:deletion-count.
Sync files originally don't have a header but headers are accepted when specified
with header=T.
base.pops
logical vector with the same length as the number of libraries
present in the sync file. Libraries indicated with TRUE will be used for identification
on the two main alleles (minor and major allele). Allele frequencies of all libraries
will subsequently be polarized for the minor allele in this specified subset.