MANTA-20 new basecall error object

incorporates sequencer error and snp prob
MANTA-20 clean up qscore init
MANTA-20 add read size to sv evidence
MANTA-20 consolidate split/paired support tests
MANTA-20 add split reads into fragment lhood
MANTA-20 account for N's in split lhood compute
MANTA-20 seperate split read portion of scoring
MANTA-20 update debug output
MANTA-20 raise float res
MANTA-20 adjust likelihood function for split reads
MANTA-20 split read adjustments

1. remove microhomology adjustments for now, these should be
treated as a range
2. more separation of alignment method from alignment data
MANTA-20 handle non-evaluated split reads
formatting update
MANTA-20 fix numerous logic errors from refactor
MANTA-20 fix more new split issues, improve debug
MANTA-20 slight efficientcy improvement
MANTA-20 tweak lhood loop
MANTA-20 adjust split read q-score handling
MANTA-20 rename methods to match MANTA-42
update cl