test SSW perforamnce; not bam will be generated
	new file:   CommonSource/PairwiseAlignment/ConvertSswToAlignment.cpp
	new file:   CommonSource/PairwiseAlignment/ConvertSswToAlignment.h
SSW outputs bam
Modify several "passing by values" to be "by references"
Modify several "passing by values" to be "by references"
Merge branch 'hash' into ssw

Conflicts:
	src/MosaikAligner/AlignmentThread.cpp
SSW scores change to be 10, -9, -15, and -1.
Mark several lines belonging to banded SW as comments
First test of hash cutoff
The previous version doesn't work so undo some changes
If the number of hashes is larger than mhp, then do not load them in
the hash table.
Remove the statement, ((std::size_t) iss.tellg()) != s.size()),
in string_converter.h
no log10 for numbers of mappings and hashes for mapping-quality training
Fix a bug that is putting wrong bases in bam for rescued mates
no log10 for numbers of mappings and hashes for PE in QualityNeuralNetwork.cpp
Bug fix for the previous version
Resolve the segmentation fault that is caused
by using cross chromosomes to rescue reads
Make aligning N's be mismatches
In the Rescue function, should not convert ssw_alignment
  if no ssw_alignment generated by ssw.
The fast version works well on 1000G phaseIII