Remove == and equals() methods from Allele class

Since this is a case class, methods are automatically provided that implement
the same logic.
Refactor likelihood calculation

This commit moves the likelihood calculation code from Pileup and Genotype into
a new singleton object.

This refactoring enables a more efficient implementation that resuses
computation between genotypes that share alleles. On my local tests, the
likelihood calculation is about 40% faster than the previous implementation.
Overall that gives about a 10% performance boost to variant calling.

 * Create a new package and singleton object Likelihood for likelihood calculation code.
 * Remove likelihood calculation code from Pileup and Genotype
 * Port tests from PileupLikelihoodSuite and GenotypeSuite into a new test suite LikelihoodSuite
 * Port variant callers to use new likelihood calculation function.

Closes #228.
Change Likelihood computation to use the Colt library.
Simplify Likelihood.likelihoodsOfGenotypes function

Always perform the calculation in log-space
formatting fix
more cleanup of likelihood testing

removing a bunch of boilerplate around converting pairs of characters
to Genotypes
Merge pull request #231 from ryan-williams/pr/229

some cleanup of likelihood testing
Better variable names in Likelihood.likelihoodsOfGenotypes
Merge pull request #229 from hammerlab/likelihood-refactor

Likelihood refactor
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
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
shade and relocate guava dependency to avoid conflicts