Trying to update picard 107 and hadoop 2.2.0
compiles and tests passes with this setup
Build paths fixed HADOOP_2_HOME env var points to Hadoop 2.2.0
Switching to Maven build
Fixing problems with new tribble API
Fixing Hadoop version incompatability: TaskAttemptContextImpl
Fixing CLI problem with missing Stringency option
Adding scm connection to pom.xml
[maven-release-plugin] prepare release 6.1
[maven-release-plugin] prepare for next development iteration
Fixing version numbers in README.txt
Updating CHANGELOG.txt for release 6.1
Fixing one problem with updated VCFInputFormat and updating package scripts
Merge remote-tracking branch: upstream/master