Novel de-dup
Clean up assembly log output
Add +/- capability to fix list parsing
1) Report confirmed bases
2) Don't fix bases unless --fix bases (still scans & reports)
3) More cleanup of assembly logging
Simplify assembler graph structure and remove some dead code for efficiency.
1) Add --defaultqual option to set default quality of bases when no quals are in BAM.

2) Handle "H" cigar operator (Hard Clip) by ignoring rather than complaining.