The new samtools (since 0.1.19, but not in earlier), by default removes
bases with quals less than 13. The result of this is that the pileup is
invalid... reads cannot be reconstructed, and well-defined parsers will
I know this has been in the docs for a long time... but it was only
recently implemented... breaking any validating parsers with warnings like
"depth is 5 but readlist contains 6 reads" ... etc.
This didn't cause us problems.... but I think a warning should be output
that the pileup format specification is *invalid* by default now.
Either that or the -Q option should be default 0... the way it was in