segfault - cause 'memory not mapped' when loading large alignment file about fastbaps

[sdwfrost]

Although I haven't tried it, as fastbaps works on SNPs only, I would use e.g. snp-sites to reduce the length of the alignment by SNPs only into a multi FASTA file - there were only c. 1500 SNPs in your example 3x4M genome dataset, which shouldn't present a problem.

[stevenjdunn]

That's done the trick - and I have been looking for something exactly like snp-sites for a while now, so double thanks are in order. Make that triple thanks including my gratitude for the speed of your reply!

Cheers.

[sdwfrost]

There's lots more that can be done with adding import filters to try to tackle these kinds of issues; closing this for now.