[Bioperl-guts-l] [Bug 2436] Inconsistencies in function HSPI::seq_inds when encountering gaps

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jan 31 14:02:02 EST 2008


------- Comment #4 from scarmi at shoshi.ph.biu.ac.il  2008-01-31 14:02 EST -------
Hello Chris
I understand your answer- if there's a double gap (or gap+mismatch) they both
belong to the same index, so only one value is reported. However, the function
'seq_inds' get as parameter the value of 'no-match', meaning that gaps should
not be reported at all! My thought was, that if I am wrong, and 'no-match'
means *both* 'mismatch' and 'gaps', then at least *all* the gaps should be
So probably the best solution is only to report the mismatches and not report
any gaps at all, when the paramter is 'no-match'. What do you think?

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