notes

AlignedContig constructor from BamRecordPtrVector
--- Makes the alignment fragments
------ Makes the indel bps from each AlignmentFragment
--- Make the SV BreakPoints
------- Makes each BreakEnd -- this will take BamRecordPtr data from AlignmentFragment into the BreakEnd (e.g. nm)
------- Makes the "local" breakpoints and "secondaries" breakpoints
------- Sets the "global" breakpoint
----------- Calls BreakPoint "set_homologies_insertions" for all global and local bps
----------- Calls BreakPoint "order" for all 
----------- Sets the BreakPoint SVType
----------- Instantiates a new Prefix : SampleInfo map

Directly from BreakPoints
--- scoreBreakpoints
------- "set_evidence" that sets DSCRD, INDEL, ASDIS, etc
------- calls SampleInfo -> modelSelection
--------------- sets the alt cov and total cov
--------------- calls the __log_likelihood for alt or err
--------------- calls the __log_likelihood for ref or alt
--------------- calls the __genotype_likelihoods for 0/0, 0/1 or 1/1
--------------- calls "score_somatic" that sets somatic_lod