…e `remove.subset` and `min.sampleNumber`. Now, NDR = 0.999 and NDR = 1 produce identical results except for the NDR threshold itself.

…DistStartEnd1/2 from opt.discovery into a new opt.rcAssignment parameter with its own setRcAssignmentParameters().

… fix

…econdaryDistStartEnd1/2 from opt.discovery into a new opt.rcAssignment parameter with its own setRcAssignmentParameters()."

This reverts commit dac871e.

…marySecondaryDist, and min.primarySecondaryDistStartEnd2, so the assignment step can be tuned independently from opt.discovery. calculateDistTable() and assignReadClasstoTranscripts() now use rcAssignmentParameters instead of isoreParameters.

…iscoveryParameters for consistency with setRcAssignmentParameters and setEmParameters naming convention.

…wrapper, include single cell .bam example, update writeBambuOutput

… this is not used in transcript discovery

fix: adjust NDR threshold behavior. Previously, NDR = 1 would overrid…

…rcAssignment

Implement opt.rcAssignment.

Single cell wrapper and removal of barcodesToFilter, sampleName, cleanReads