wrap some long lines
EoF newlines
name a boolean param
use '_' shorthand
specify 0-based indexes on Read.start
verify inserted/reference bases in PileupSuite
check insertion bases in PileupSuite
Merge pull request #148 from hammerlab/style

a few more style nits I had laying around
Merge pull request #149 from hammerlab/pileupsuite-nits

Pileupsuite nits
Merge remote-tracking branch 'origin/master' into option-ify

Conflicts:
	src/main/scala/org/bdgenomics/guacamole/reads/Read.scala
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