shade and relocate guava dependency to avoid conflicts
scope Caller and Arguments inside companion object

this makes for a messy diff but sets up the auto-parsing of cmd-line
args for Guac commands
fold Args4j.apply into Command
make Command inherit Serializable and Logging
add GermlineCallerArgs
unroll wildcard guacamole imports
add SomaticCallerArgs
provide SparkCommands with SparkContexts
add SparkContext.stop() to SparkCommands
update “variant caller” language in Command
wrap sc.stop() in a try/finally block
get read input from adam records
adding additional test for cases where inferredinsert size is none
Fix coalescing of adjacent or overlapping intervals in LociMap

 * Add a test case to LociMapSuite that fails with the old implementation of LociMap
 * Fix LociMap.Builder.result() so the test now passes.
Add LociSet.SingleContig.Iterator class

Implements an iterator for loci on a single contig, and adds tests for it.
Replace LociInWindowsIterator

This commit drops the LociInWindowsIterator class, adds the
SlidingWindow.advanceMultiple function as a replacement, and modifies
DistributedUtil to use this function.

The primary motivation for this is readability, but there is also a subtle bug
fix here.  The hasNext() function on LociInWindowsIterator wasn't correct in
general, since if skipEmpty=true, then it is impossible to know whether there
are really more regions available to advance to without actually doing the
advancing. (For example, suppose we have a window at locus 100, the next region
to be read by that window is at locus 150, and we want to advance to position
1000. It is impossible to know if there are in fact regions at locus 1000
without first advancing through the region at locus 150.)

Closes #214.
Merge pull request #245 from ryan-williams/command

Move Command boilerplate into SparkCommand
double-dash, dash-case all command-line options
drop unused PoCIndelCaller

fold PoCIndelCaller’s tests into SomaticStandard’s

fixes #207
Minor comment fixes, remove unused imports