Reordered files
AlignmentCoverage now uses the CIGAR.

In addition to the regular coverage, it takes into account the offset of a
deletion or insertion.
Added length in AlignmentDifference.

When the difference is too large, it is not stored completely.
Now AlignmentDifference might not store reference sequence.

To use AlignmentDifference.seq now, you will have to ask if in this
AlignmentDiference isSequenceStored().

This was done to improve performance in those algorithms where you need CIGAR
information, but not the reference sequence of the read. This way we avoid
asking it to cellbase in every alignment.
Now AlignementHelper can handle a null reference sequence.

If getDifferencesFromCigar recieves a null as refStr, it means that it is not
needed to store the reference sequence in the AlignmentDifference(s).

Updated AlignmentSamDataReader.