Wrong alignment retained in agreement step (gene ZBTB10) #35
Description
The factorization step of PIntron computes, for RefSeq NM_023929 (gene ZBTB10), the annotated spliced alignment (with 7 exons) and an "false" alignment (with 6 exons). The agreement step retains the wrong alignment with 6 exons.
Both alignments have 0 errors and 100% coverage, but the second one has a non-canonical GG-TA intron, while all the annotated introns are canonical GT-AG or GC-AG.
PIntron version: v1.2.55
Input files: https://gist.github.com/4593092