(unless I'm missing something subtle- see image below)
can be forced into intuitive compliance by increasing the threshold param or by flipping into
smith-waterman mode, but no user wants to learn how to do that!
this is going straight to the icebox, just wanted to get it noted before it lapsed into oblivion;
I do find the repeat algorithm over-aggressive on occasion, but this case seems like it is just
arbitrarily thumbing its nose at William of Occam (which brings to mind a scene from the film Chinatown)
"Fixed" in commit ffc8c4a5332ba667528365cee1b7f1a0b356df48. I use quotes because it's still possible for spurious inversions to occur, just now they're very unlikely.
e.g. http://laasi.ncgr.org/mt_hapmap/gcv/#/search/mt_hapmap/medtr.HM129.v1.0.g1216?regexp=&neighbors=10&sources=mt_hapmap&alpha=0.5&kappa=10&minsup=2&minsize=5&matched=4&intermediate=5&algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&threshold=25&order=chromosome
(unless I'm missing something subtle- see image below) can be forced into intuitive compliance by increasing the threshold param or by flipping into smith-waterman mode, but no user wants to learn how to do that! this is going straight to the icebox, just wanted to get it noted before it lapsed into oblivion; I do find the repeat algorithm over-aggressive on occasion, but this case seems like it is just arbitrarily thumbing its nose at William of Occam (which brings to mind a scene from the film Chinatown)