Changed first-line processing by preparePairs to return original alignment positions and lengths.
Modified getPairData function (added C++ code) to pull out insert sizes, orientations, fragment lengths from processed files.
Modified check_input so that it no longer checks the count field. Modified registration functions to reflect new code.
Removed all dependencies on an incoming count field, during read counting for margins/region pairs/bin pairs.
Added a pairParam class to standardize restriction fragment input, restricted lists, discard regions.
Added support for discarding reads in blacklisted regions in .baseHiCParser, switched to accepting pairParam.
Added support for param inputs/discarding reads in counting functions.
Switched to param input for boxPairs.
Added support for param input, discarding reads in plotPlaid and rotPlaid.
Eliminated dependence on .sortedAggregate in savePairs.
Removed aggregation of counts in mergePairs.
Changed countPairs function to prunePairs, switched to param support, optimized some code.
Moved csaw dependency to suggests, added new functions, classes for export.
Added check for prunePairs read pair removal, read pair discarding in blacklisted regions.
Modified count simulator defaults; added augmentsim function to simulate alignment positions and lengths.
Removed counting tests from tests for preparePairs, added more tests for getPairData.
Removed counting tests, added support for random fields in savePairs and mergePairs.
Small change to boxPairs test, to reflect new parameter format.
Changed counting tests to accept new parameters, reflect new simulation design, lack of counts in input files.
Added warning when column names in mergePairs are not identical.