MANTA-20 first progress on breakend aligner
MANTA-20 refresh formatting
MANTA-20 more progress incorporating single-region contig aligner
MANTA-20 completed first pass on a basic single-region contig aligner
MANTA-20 add test code, clean-up doc details
MANTA-20 minor optimizations to the global aligner, generalize shared sections of code
MANTA-20 switch to lower-memory implementation of the aligner
MANTA-20 starting work on jump aligner
MANTA-20 progress on the jump aligner..
MANTA-20 finish debugging jump aligner and add tests to lock down expected behavior
wqMerge branch 'master' into MANTA-17