Turn off fixmate for Bwamem

This adds a method 'requires_fixmate' in AlignmentResult.pm to control
running fixmate after alignment. Aligner submodules can disable fixmate
by overriding the method 'requires_fixmate' and returning 0. An old
check for disabling fixmate for Rtg aligners in AlignmentResult.pm has
been removed, and the Rtg aligner modules now override the
requires_fixmate method. Bwamem also overrides the method, since fixmate
is incompatible with the 0x800 supplementary alignment flag that Bwamem
uses.
Max af filter
Merge branch 'updated' into gb_master