MANTA-17 add operator<< for Alignment, move alignend
MANTA-17 add operator<< for contig
MANTA-17 add debug output for alignment results
MANTA-17 semi-temp debug code to start getting deletions assembled
MANTA-17 setup all read reversals, breakpoint reorderings to (in theory) correctly build contig and align for all 2 breakend SV types