Partition load bug fixed

Load_DB was incorrectly testing db->cutoff before it had been set.
Bug fix in QV.c

The way the default substitution character was determined meant that if
there is a run length that only occurs in the first 100K characters,
then it has no code.  Fixed so that every possible run length has a
code.
QV.c modification

The problem with Pacbio deletion Tags was fixed more elegantly by
modifying detract.  So code added to QV.c to detect the problem (which
no longer occurs) has been removed.
Pulses: short -> int in DB.h
Small format error for alignment printing fixed
Merge remote-tracking branch 'upstream/master'