daligner -M option, compiler warning clean up

Most of the changes are code refactoring so that most versions of gcc
do not emit warnings during make.

The -M option, that implicitly sets a value of -t based on an
examination of the k-mer frequencies in the blocks has been added to
daligner.

Daligner now will work on memories larger than 16Gb simply by using
int64 instead of int32 variables in the appropriate places within the
code.

The alignment finder of align.c uses a new termination criterion which
no longer requires the specification of a minimum correlation and
actually makes its behavior more robust through low quality read
segments (i.e. few containment and gapped overlaps).
Merge remote-tracking branch 'upstream/master'

Conflicts:
	Makefile
update filter_p.c