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
pass reference base to pileup instead of rebuilding; drop saving of mdtag