Testing CMS as a k-mer counting prefilter.
Cache solid k-mers during error correction using a bloom filter
Testing simpler string graph haplotype builder
Testing new methods of extracting reads/overlaps from the index
Built framework to abstract away the read extraction/overlap computation during string graph hap gen
More abstraction of read extraction code
Merge branch 'probcache' into new-overlap-hapgen

Conflicts:
	src/Util/Makefile.am
code cleanup
Variant caller now writes out a bam file containing evidence for each variant
Various bug fixes for evidence bam output
Code cleanup
When outputting a projected BAM, handle the case where the haplotype and reference do not align end-to-end
Updateed third party code
Correctly set the strand information when outputting evidence BAM
Output read names in evidence BAM
Code cleanup
Ported DindelRealignWindow to use new MultipleAlignment class instead of deprecated MultiAlignment
Rewrote DindelHaplotype::extractVariants to use new MultipleAlignment data structures
Turned on semi-global alignment
Working on improving the haplotype-to-reference alignment