Alpha 6.14: Ambiguous-sex + sample-filter bugfixes, duplicate-sample-ID segfault fix

This fixes several sex-affected calculations which could be incorrect when ambiguous-sex samples were still present after some samples were filtered out. (The bug did not affect runs where ambiguous-sex samples were present but the main sample filters didn't do anything.)

It also fixes a segfault that could occur after a "Duplicate sample ID" error message was printed.