Added switches to spark context creation code to allow buffer size increase and increased logging for profiling.
Merge pull request #161 from fnothaft/context-debug

Added switches to spark context creation code
Add util.BuildInformation and buildinfo command

This is a first attempt at #41.

- adam-core: Add git-commit plugin to POM file. The file is generated
is `adam-core/src/main/resources/git.properties` and the info is
available in the object
`edu.berkeley.cs.amplab.adam.core.util.BuildInformation`.
- adam-cli: Add the command `buildinfo`.
Merge pull request #138 from smondet/git_properties

Display Git commit info on command line
Remove extraneous initLogging() calls
Upgrade to Spark 0.9 and Scala 2.10
Workaround apparent changes to implicit resolution
Upgrade to Java 7. Resolves #134
Upgrade to Parquet 1.3.2. Resolves #94
Merge pull request #78 from jey/spark-0.9-upgrade

Upgrade to Spark 0.9 and Scala 2.10
Refactoring FASTA work to break contig sizes.
Merge pull request #160 from fnothaft/fix-fasta-large

Refactoring FASTA work to break contig sizes.
call PluginExecutor in apply method, fixes issue 164
Merge pull request #165 from heuermh/plugin-listdict-fix

call PluginExecutor in apply method, fixes #164
fix typo in log4j config, but junk is still spewed to stdout
Remove existing BQSR implementation
Make quality scores into ints
Scaffolding for BQSR implementation
add Util.hashCombine
add stuff to Observation