--zip-out triggers segfault if not provided with an integer value

[bs-az]

Here is the doc-string for --zip-out:

    --zip-out         STR/BOOL    Optional  Controls the output compression                       Yes/True

       By default the report files are produced in the same format as the input i.e.
       if the reads files are compressed (gz), the output is also compressed.
       The default behaviour can be overriden by using '-zip-out'.
       The possible values: Y(es), N(o), T(rue), F(alse). No value means 'True'.
       The values are Not case sensitive i.e. 'Yes, YES, yEs, Y, y' are all OK
       Examples:
       '-reads freads.gz -zip-out n' : generate flat output when the input is compressed
       '-reads freads.flat -zip-out' : compress the output when the input files are flat

This is inconsistent with the source code at options.cpp#L1139

void Runopts::opt_zip_out(const std::string& val)
{
	if (val.size() > 0) {
		auto ii = std::stoi(val);
		if (!(ii == -1 || ii == 0 || ii == 2)) {
			WARN("'", OPT_ZIP_OUT, "' can only take integer values: [", -1, ", ", 0, ", ", 1, "]. Provided value: ", val, " Using default: ", zip_out);
		}
		else {
			INFO("using '", OPT_ZIP_OUT, "' with specified value ", ii);
			zip_out = ii;
		}
	}
}

std::stoi will trigger a segfault when provided with e.g. --zip-out No

[biocodz]

Good catch! Thanks for reporting.

[biocodz]

Fixed in commit 580d0872b1f144fbf81d7987124c693f6cbda12a. To appear in release 4.3.5 (soon)