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I've explicitly added C99 to the build settings and fixed the one simple non-compliance issue.
I've also run splint on the code to generate a C99 compliance report. It returns the list of issues below. Not all are to do with C99 compliance. I've looked into each of the issues reported and am happy that, in our case, they're false-positives. As an example, there's a false-positive where we
gzclose
a file descriptor stating that the memory is not free'd. The zlib library call and the kseq_destroy call ensure (as much as can be ensured) that memory is free'd.