abstract out sliding window for any genomically mapped object
renaming read to region where applicable
fix test expected error message
new snv caller
adding caller to main list
filtering out deletion alternate base for now
more updates of comments and variable names from read to region
update for ADAM 0.11
change reference region to hasreferenceregion
Merge pull request #139 from hammerlab/slidingwindow

Generalize SlidingReadWindow to SlidingWindow over regions
Merge pull request #134 from hammerlab/simple-snv

Somatic SNV caller using base and alignment qualities
upgrade scalatest

supports wildcard single-{test,suite} running, e.g.:

mvn -Dsuites='*PileupSuite' test
mvn -Dsuites='*PileupSuite qualities' test
remove redundant 'val' keyword
use .count instead of .filter.length

intellij suggests this; seems cleaner/simpler
add EoF newlines
break long-line of inheritance declarations
use nonEmpty instead of !.empty
simplify match statement, avoid return statement

IIRC, return statements are implemented using exceptions, and are
relatively unperformant as a result; also stylistically at odds with
functional code flow
group loci statements to match other callers

in some world we may want to reuse this boilerplate across VCs
fix variable shadowing

intellij doesn't like shadowed var names, seems reasonable