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this refers to the sequence search in javascript. We align to root using a stupid string matching routine and then look for mutations. If the query has a gap relative to root, no proper alignment is found.
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trvrb commentedon Dec 23, 2015
Can you say more? You'd like an alignment that maintains gaps? Wouldn't numbering get very complicated in this case?
I guess you could do an alignment that allows gaps then build the tree then remove gaps to get canonical numbering.
rneher commentedon Dec 23, 2015
this refers to the sequence search in javascript. We align to root using a stupid string matching routine and then look for mutations. If the query has a gap relative to root, no proper alignment is found.
trvrb commentedon Sep 23, 2017
This has been resolved in the nextstrain/augur codebase.
rneher commentedon Sep 23, 2017
I don't think this is resolved. It also refers to sequence search/alignment in auspice rather than augur. This should be a feature request in auspice. I did write a proper pairwise aligner a while back: https://github.com/neherlab/timetree_viewer/blob/master/js/alignPairwise.js
trvrb commentedon Sep 23, 2017
I see. Thanks Richard. Just reopened.