Time-series reciprocal mapping

[elizabethmcd]

Current mapping functionality only maps 1:1 for sample reads:assembly, with a time-series want to reciprocally map to all samples to get differential coverage information

[elizabethmcd]

--time-series flag for reciprocal mapping for differential coverage/abundance, and summary plots that show this information. This will have to be tested with a different test profile conf and dataset that is actually part of a time series to make sure everything is working

[elizabethmcd]

Make a mapping flag either --mapping self or --mapping reciprocal with the self option as default to only do 1:1 mapping for corresponding reads:assemblies, whereas reciprocal will be for time-series all-v-all