Whilst somalier is responsible for telling us the similarity between each file - we need to come up with an algorithm for what to do with that information.
Index files are compared to every fingerprint in the database (including themselves).
For each comparison somalier returns a variety of statistics - in
particular N (the count of site matches) and relatedness (a score of similarity at those sites, with
one meaning identical).
Index file names are also compared to the filename of every fingerprint in the database - using
a regular expression. If every capture group of the regular expression matches between the
file names then we return a regexMatch of true, else false (for example, we can set a regex
to match of the SUBJ_xxxx part of the filename).
if (regexMatch and relatedness < threshold)
return Unexpected Unrelated { relatedness }
else {
if (relatedness >= threshold and N > minimum N) {
# passing these thresholds means
# we believe these refer to the same sample with a degree of confidence
if (regexMatch)
# we may not report out Expected Related
# but it is useful to return the value of relation
return Expected Related { relatedness }
else
return Unexpected Related { relatedness }
}
}