mpileup: Allow up to five alleles (N,A,C,G,T)
New "flags" command plus moved filtering from htslib/pileup to BAM reading callbacks
On behalf of Peter Chines, test that filter mask replaces (not just adds to) default mask
mpileup: Disabled CDF version of MWU annotations and made it optional at compile time
Merge branch 'develop' into calling
Merge branch 'calling' into develop