Add multiple compartments / populations and genome transfer #32
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remove recursion testing edit edit removed randomness removed randomness i - 1 removed infinity
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This long overdue pull request adds the ability to use multiple compartments in simulations and genome transfer between compartments. To implement this, I had to change the upper level program flow of SANTA-SIM substantially to go use my new santa.simulator.compartments.Compartment class. However, I ensured that the software is still backwards compatible.
Genome transfer is implemented via a transfer probability matrix where the probabilities are constant ( or dependant on a fitness function. Genome transfer can also be done at specified times using the TimedTransfer class.
Compartments and the Transfer options can be specified in the XML specification file. An option to include the last time of genome transfer can be added to a sequence name when sampling alignments. There is an example at examples/HIV-1_latent.xml.
Other changes: