add better intro in README
Add example for running Guacamole on a cluster
readme fixes
Add scripts/logs4j.properties file
nit: get is not needed
readme tweak
Merge pull request #219 from hammerlab/errant-get

nit: get is not needed
Merge pull request #218 from hammerlab/update-readme

Update readme
readme typo fix
Bump java version dependency in pom 1.7 -> 1.8

Although Guacamole builds with either java 7 or java 8, the resulting jar file is too large (or has too many files) to run with java 7.

It seems odd to require java 8 to run but java 7 to build, so this commit changes our pom to specify java 8. It avoids specifying an exactly version, but instead just specifies 1.8. I've seen some examples of this in other project's pom.xml files but am not completely sure it is right.
Merge pull request #222 from hammerlab/bump-java-to-1.8-in-pom

Bump java version dependency in pom 1.7 -> 1.8
adding yourkit image
Merge pull request #226 from hammerlab/yourkit

Adding yourkit image
Speedup Pileup.atGreaterLocus by using a vector for PileupElement

Seq in scala defaults to a List implementation, which takes O(n) time for
append. This commit changes Pileup to use a Vector-backed Seq for PileupElement
instances, which makes Pileup.atGreaterLocus much faster. The interface to
Pileup stays the same.

On my single-node tests, this gives about about a 20% speedup in overall
variant calling time (on one test: 5 min 7 sec -> 3 min 55 sec).
get reference as seq bytes from mdtag
Merge pull request #220 from hammerlab/md-tag-bytes

get reference as seq bytes from mdtag
Small tweakes in Pileup.atGreaterLocus()
Merge pull request #227 from hammerlab/pileup-elements-should-be-vector-not-list

Speedup Pileup.atGreaterLocus by using a vector for PileupElement
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.