It would be great to have the option to have all internal schemes run on a sample either through the existing interface of --scheme all or another flag. BioHansel would then test a sample against all of the schemes and then report the best scoring scheme results. Based on the existing code, it would be a major refactor to have it report kmer results on a per scheme basis as an integrated report, so I would think that either reporting just the top-scoring scheme or have the output files append the scheme name to each output would be the easiest solutions. This would make it easier for people to use in IRIDA? What do you think @peterk87 @apetkau ?
It would be great to have the option to have all internal schemes run on a sample either through the existing interface of --scheme all or another flag. BioHansel would then test a sample against all of the schemes and then report the best scoring scheme results. Based on the existing code, it would be a major refactor to have it report kmer results on a per scheme basis as an integrated report, so I would think that either reporting just the top-scoring scheme or have the output files append the scheme name to each output would be the easiest solutions. This would make it easier for people to use in IRIDA? What do you think @peterk87 @apetkau ?