segfault from C stack overflow about fastbaps

[gtonkinhill]

Hi,

This is probably due to the very large number of SNPs in your alignment. The fasta load function was written for speed and optimised for slightly shorter alignments. A work around is to use the ape function read.FASTA and pass this to the fastbaps import function as

msa <- ape::read.FASTA('/path/to/msa.fasta')
sparse.data <- fastbaps::import_fasta_sparse_nt(msa)

If your alignment includes non-varying sites I would also recommend first running snp-sites.