the code in NpzSNPSource._guess_filename_format was supposed to be able to detect s_padding == r_padding == 0 when zero-padding is not used in these indices
however, this was based on the false assumption that os.walk will always return the shortest paths first, which was false: for example, if os.walk first returns a directory like "scenario_15" it would assume that s_padding == 2, even if there is no directory like "scenario_09" as opposed to "scenario_9"
(this bug applies to the full file path as well; I am just using directory names as an example in the above paragraph)
Edited by E. Madison Bray