PeakQuery to flag read peak sequences as plus strand. Updated ProbeGenerator to orient all probes according to the PWM. Reasonably extensive bugfixing of genome util package to properly handle cases of Mutating and Joining probes that are on the minus strand or different strands. Added several methods to GenomicSequence for correctly dealing with coordinates in plus strand space, but sequence from the minus strand. Chiptools Probes data class also updated to correctly mark binding sites and mutations on probes with minus strand sequence.
updated GCRunMutator function to deal with probes on the minus strand. Appears to work correctly now.