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EddyRivasLab / infernal

RNA secondary structure/sequence profiles for homology search and alignment
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cmbuild --refine bug related to fragments #42

Closed nawrockie closed 5 months ago

nawrockie commented 5 months ago

If the input MSA has fragments with missing data characters at the 5' and/or 3' ends and --refine is used with cmbuild, the program with crash with a segmentation fault.

nawrockie commented 5 months ago

Bug was due to the cmbuild.c local function convert_parsetrees_to_unaln_coords(), which is only called if --refine is used, not treating missing data characters as gaps. This is relevant only since the addition of sequence fragment support, denoted by missing data characters at the 5' and 3' ends, in alignments, which was added between releases 1.1.4 and 1.1.5.

Fixed as of 039db6b