Change output format to show Genotype rather than Alt Base

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

http://sanger-pathogens.github.io/snp-sites/

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Change output format to show Genotype rather than Alt Base #19

Closed bewt85 closed 9 years ago

bewt85 commented 9 years ago

Part of ticket 471874

Previously snp_sites reported the value of the alternate base if present else returned '.' if the base matched the reference sequence. Unfortunately some tools (like Plink and PyVCF) did not understand this format. I've therefore implemented the suggested Genotype format in the spec.

This is a breaking change so I've bumped the VERSION to 2.0.0

bewt85 commented 9 years ago

@satta, if you have a minute, would you mind reviewing this for me?

bewt85 commented 9 years ago

closed while I make changes discussed with @satta

bewt85 commented 9 years ago

@satta I've made most of the changes we discussed. I've not removed the exit because this is already taking too long and it doesn't add loads of extra value (probably).