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Adding New distances
Martin Vickers edited this page Jul 1, 2022
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Add additional distance measures that use k-mer counts is very easy. If you wish to request a new measure, please raise a github issue.
If you'd like to attempt to implement one yourself and submit a pull request we would be very happy to receive this. A distance measure is implemented in the distance.cpp file, the header.h must be defined and finally the --distance-type options need to be set it the following places;
- https://github.com/martinjvickers/KAST/blob/7ad39513bd0aa5a31641436efbc6f8af206e58bc/utils.h#L52
- https://github.com/martinjvickers/KAST/blob/7ad39513bd0aa5a31641436efbc6f8af206e58bc/search.h#L204
- https://github.com/martinjvickers/KAST/blob/7ad39513bd0aa5a31641436efbc6f8af206e58bc/search.h#L241
- https://github.com/martinjvickers/KAST/blob/7ad39513bd0aa5a31641436efbc6f8af206e58bc/pairwise.h#L44
- https://github.com/martinjvickers/KAST/blob/7ad39513bd0aa5a31641436efbc6f8af206e58bc/pairwise.h#L329
- https://github.com/martinjvickers/KAST/blob/7ad39513bd0aa5a31641436efbc6f8af206e58bc/pairwise.h#L410