Streamlined SISRS Log that supports checkpointing

[BobLiterman]

Certain tools in the SISRS pipeline (namely BAMTools) can fail for one reason or another and don't throw an explicit error when it happens. This makes restarting SISRS after 1 failed step cumbersome.

I will think about a solution where SISRS exports relevant information out into a clean log, INCLUDING parseable lines that could be used to detect breakpoints.