Pileup.Element: ignore `P` CIGAR-operator

It can be ignored: http://davetang.org/wiki/tiki-index.php?page=SAM
and it is the simplest way of dealing with it correctly (if we want to
keep the padding information in the future, we will need a more complex
`Alignment` case class).
Add more tests for Pileup.Element
Pileup: add comments and rename variables
Merge pull request #55 from hammerlab/pileup_fix_and_tests

Pileup fix and tests
Threshold caller outputs OtherAlt calls appropriate. Closes #15
change default -loci arg from 'mapped' to 'all'
bump java memory in scripts/guacamole
add emitRef and emitNoCall options to Threshold variant caller
small optimization to LociMap builder
sliding window no longer warns if there are no reads in a window
DistributedUtil improvements.

Fix serious bug in partitionLociUniformly that could cause an infinite loop. More tests.

Better implementation of windowTaskFlatMap.
minor tweaks to splitLociUniformly
introducing counters
Dropped counters, going with DelayedMessages instead
Got rid of any usages of scala's NumericRange type, which in some cases can end up making a giant array for all the integers in a range (and also can't work with Longs correctly). Replaced with LociMap.SimpleRange.
formatting, comments
another partitionLociUniformly test
comments and formatting