update tests from deprecated syntax
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
swap getMappedReadOpt in for getMappedRead
sequencedSingleBase returns Option, doesn't throw
getMappedReadOpt change that got lost in merging
rename mdTag{,String} fields to reflect Optionness
move Read.scala into its own 'reads' package

- it has a lot of classes in it already, which I would like to break
out
- org.bdgenomics.guacamole package becoming a bit of a kitchen sink
- prefer code only in "leaf" packages
put {Un,}MappedReadSerializer in their own files
case-class-ify MateProperties

- put an optional instance in each of {Un,}MappedRead
  - it is Some() iff former isPaired boolean would have been true
- give it its own ser/deser classes, called by *MappedReads'
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
PR feedback
Merge pull request #146 from hammerlab/matchers

Update tests from deprecated syntax