Refactor splice junction counting

We count and store splice junctions always, and filter on demand. This is actually only true for minJunctionCoverage and ignoreStrandedness; we still filter based on minFlankingWidth upon loading (needs revisiting)
Have IgvTools.run throw its preprocessing exception instead of just logging it
Move optional arguments to the bottom of window in bedtools_plugin

IGV-1957
Merge pull request #48 from broadinstitute/KeepSpliceJunctions

Refactor splice junction counting
Update BEDToolsPluginSourceTest for new argument order

Further modify bedtools_plugin.xml to OptionalArguments is at end for ALL commands

IGV-1957