add max read depth filter;other filter updates
comment/function name fixes
Merge pull request #129 from hammerlab/maxreaddepth

Add max read depth filter and remove others
make scalariform tolerate dangling close-parends

scala style guide doesn't seem to have strong guidance here,
and occasionally it feels clearer to allow parends to surround
code blocks visually in a similar fashion to the way curly-braces
commonly do (often in scala one can do as much between parends as
between curly-braces)
Merge pull request #133 from hammerlab/style

make scalariform tolerate dangling close-parends
prototype of structural variant caller