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read_fasta_file_short_names crashes when chromosome name does not have spaces #38
Description
read_fasta_file_short_names under smithlab_os.cpp uses the find_first_of function to call a substring of the chromosome name. When the name doesn't contain spaces it returns string::npos and it throws a runtime error because the end iterator is before the start iterator (which we add 1 because of the > character).
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guilhermesena1 commentedon Jul 3, 2021
I pushed a fix at 17d21f3 , which checks if there is a space and depending on whether or not it finds it, pushes the entire name or takes just the first word. Since this check is only made when we see the chromosome character (>) this should not make the function any slower. Every program that uses this function probably should be updated.