Closed lutteropp closed 5 years ago
Already checked to added approximate seed matches, those are fine.
Narrowed it down to the exact seeds themselves - why do they contain the dollar sign? Shouldn't all dollar signs be set to false in the presence checker???!!!
Checked the entire LCP array, the dollar signs are definitely not parts of any LCP. This is getting weirder and weirder.
This is getting interesting, I like this bug :-) Figured out the culprit is the trivialExtensionSimple function which looked so innocent!
datasets that seem to be affected by this bug:
the bug seems to only occur when doing trivial extension to the left - doing trivial extension to the right seems to be fine
nope, apparently it has to do with getAverageSeedSize, not with the simple trivial extension
This was a highly interesting bug indeed. The problem was the following (see attached file) leftExtension.pdf
Found the reason when trying to open the msa with old RAxML: ERROR: Bad base ($) at site 203901 of sequence 1