formatting update
MANTA-17 remove AssembleSVBreakend
MANTA-17 provide reference to SV estimation step
MANTA-40 add new rna mode and python bplate
MANTA-40 ignore anom proper-pair option for rna
MANTA-53 enable rescore option
MANTA-53 fix typo
MANTA-42 restore assertions
MANTA-42 fix candidate indexing error
remove outdated define
MANTA-42 more detailed breakend evidence tracking
MANTA-42 debug log improvements
MANTA-42 proposed index fix
MANTA-42 fix the index fix...
MANTA-42 improve error msg detail
Add cigar to BAM record dump
MANTA-42 improve read pair scanner

include local events from remote read when available
MANTA-42 fix tandem-dup pair mismatch
MANTA-42 pre-merge details
MANTA-42 fix double-canidate issue

Read pairs with multiple incompatible candidates were triggering
pair-candidate mismatch errors downstream. This patch allows for the
mismatch to occur in the (rare) instances of multi-candidates.

Also added confident pair counts.