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tseemann / snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment
GNU General Public License v3.0
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Segmentaion fault error on snp-dists v0.4 #19

Closed sseby closed 6 years ago

sseby commented 6 years ago

Hi, I am using the fasta alignment from from Gubbins as input to snp-dist. I would like to exclude Ns and include only ATCGs in the calculation. I see that snp-dists v0.4 has an option to do this, but this version fails giving segmentation fault error. Appreciate if you could please give some guidance on how to solve this issue ? snp-dists v0.2 works fine, but I do not want to use that since it doesn't have the option to exclude Ns.

Thanks, Sandra

andersgs commented 6 years ago

Hi @sseby:

Edit the following line in snpdists.h:

#define MAX_SEQ 1000000

Make that value 1000.

Recompile, and try again.

Best. Anders.

tseemann commented 6 years ago

I only support official releases on snp-dists.

https://github.com/tseemann/snp-dists/releases

The current version is 0.2

tseemann commented 6 years ago

This was fixed in #9