shade and relocate guava dependency to avoid conflicts
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.
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
Merge pull request #250 from ryan-williams/args

double-dash, dash-case all command-line options
Merge pull request #251 from ryan-williams/indel

drop unused PoCIndelCaller
Improve and update documentation

 * Tweak documentation in a number of places.
 * Add brief package level documentation. Closes #221.
 * Fix scaladoc references (no more warnings).
fix tests to write tmp file in test dir; pr feedback for base quality conversion;
pass reference base to pileup instead of rebuilding; drop saving of mdtag
test fixes; updated cigar/sequence to match mdtag in test reads
documenting parameter to Pileup.atGreaterLocus
Comment tweaks in SlidingWindow
LociSet.SingleContig.Iterator is now a BufferedIterator. Remove some methods and make others private.
Tweak documentation in windowing package.
Merge pull request #248 from hammerlab/windows-iteration-refactor

Refactor LociInWindowsIterator