Add -lociFromFile argument to Commmon

 * Any caller that uses Common.Loci set of arguments now supports a -lociFromFile argument that accepts a path to a file giving loci to call at. Closes #232.
 * Loci parsing now ignores all whitespace (including newlines, etc.) instead of just spaces.
 * Add a test for parsing a file with containing loci
Remove unused import
upgrade args4j and add forbids argument to loci args
Merge pull request #237 from hammerlab/add-loci-from-file-common-argument-forbids

Upgrade args4j and add forbids argument to loci args
Merge pull request #235 from hammerlab/add-loci-from-file-common-argument

Add -lociFromFile argument to Common
Let Travis post to #build Slack room
Integrate scoverage tool into pom.xml

Followed instructions at: https://github.com/scoverage/maven-scoverage-plugin

After running "mvn test", an HTML coverage report can be generated by running
"mvn scoverage:report". The result will be written to target/scoverage-report.

scoverage currently does not support line-by-line code coverage reports when
using Scala 2.10.4 (our version). However, we can still get a per-class
coverage report. When we update Scala to either 2.10.5 or 2.11.2, this should
be fixed, according to
https://github.com/scoverage/scalac-scoverage-plugin/issues/16

As part of this, I also ended up reformating pom.xml to use 2-spaces throughout.
Generate and publish test coverage report using travis

In addition to the scaladoc, Travis will now push to the gh-pages branch a
"scoverage-report" directory giving our code coverage report.

Closes #212.
Fix scoverage publishing to gh-pages with travis
Merge pull request #241 from hammerlab/add-scoverage-tool

Add scoverage test coverage tool
Update pom.xml

add newline to pom.xml
Move scoverage into "coverage" profile in pom

Code coverage can now be generated by:
```
    mvn package -P coverage
    mvn scoverage:report
```

It will also be generated when running under Travis CI (by checking the TRAVIS
environment variable).
Merge pull request #240 from ryan-williams/slack

Let Travis post to #build Slack room
Merge pull request #243 from hammerlab/move-scoverage-to-profile

Move scoverage into "coverage" profile in pom
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