The phasing_hmm class defines std::vector < char > VAR_TYP; it uses this to hold signed values for example :

#define VAR_PEAK_HET 0
#define VAR_PEAK_HOM -1
#define VAR_FLAT_HET -2

The problem is that the C/C++ standard does not define char to be signed or unsigned.
See : https://stackoverflow.com/questions/2054939/is-char-signed-or-unsigned-by-default

This is also documented in the GCC manual here https://gcc.gnu.org/onlinedocs/gcc-4.2.2/gcc/C-Dialect-Options.html :

"Each kind of machine has a default for what char should be. It is either like unsigned char by default or like signed char by default.

Ideally, a portable program should always use signed char or unsigned char when it depends on the signedness of an object. But many programs have been written to use plain char and expect it to be signed, or expect it to be unsigned, depending on the machines they were written for. This option, and its inverse, let you make such a program work with the opposite default.

The type char is always a distinct type from each of signed char or unsigned char, even though its behavior is always just like one of those two."

For GLIMPSE what this means is that if it is compiled with a compiler or machine that defaults char to unsigned, multiple tests will fail, see the example below :

The value is used in void phasing_hmm::forward() and void phasing_hmm::backward() e.g., :

		if (VAR_TYP[curr_idx_locus] >= VAR_PEAK_HET) {
			if (curr_idx_locus == (VAR_TYP.size()-1)) INIT_PEAK_HET(VAR_TYP[curr_idx_locus]);
			else if (curr_segment_locus != (segments[curr_segment_index]-1)) RUN_PEAK_HET(VAR_TYP[curr_idx_locus]);
			else COLLAPSE_PEAK_HET(VAR_TYP[curr_idx_locus]);
		} else if (VAR_TYP[curr_idx_locus] == VAR_PEAK_HOM) {
			if (curr_idx_locus == (VAR_TYP.size()-1)) INIT_PEAK_HOM(VAR_ALT[curr_idx_locus]);
			else if (curr_segment_locus != (segments[curr_segment_index]-1)) RUN_PEAK_HOM(VAR_ALT[curr_idx_locus]);
			else COLLAPSE_PEAK_HOM(VAR_ALT[curr_idx_locus]);
		} else if (VAR_TYP[curr_idx_locus] == VAR_FLAT_HET) {
			if (curr_idx_locus == (VAR_TYP.size()-1)) INIT_FLAT_HET();
			else if (curr_segment_locus != (segments[curr_segment_index]-1)) RUN_FLAT_HET();
			else COLLAPSE_FLAT_HET();
		} else vrb.error("Unknown variant type in phasing backward pass at variant " + stb.str(curr_idx_locus));

If char is unsigned the test if (VAR_TYP[curr_idx_locus] >= VAR_PEAK_HET) will always succeed as VAR_PEAK_HET is defined as 0. This is not the desired behaviour.