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sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file
http://sanger-pathogens.github.io/snp-sites/
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Add output of only count of constant sites #84

Closed pvanheus closed 4 years ago

pvanheus commented 4 years ago

I was discussing with some colleagues computing the count of constant sites in an alignment (for input to the -fconst option of IQ-TREE) when @tseemann suggested adding a routine to snp-sites. This PR adds that routine using the -C flag. The version number is not changed in this patch but feel free to merge the code if you think it is useful.

pvanheus commented 4 years ago

I did not add a test for this code because I do not quite understand how the testing system works.