Changing hadoop fs call to be compatible with Hadoop 1.
Merge pull request #76 from bigdatagenomics/hadoop-1-fs-compatibility

Changing hadoop fs call to be compatible with Hadoop 1.
Update README and cleanup top-level cli help text
Merge pull request #81 from bigdatagenomics/matt-cleanup

Update README and cleanup top-level cli help text
Merge branch 'master' of https://github.com/bigdatagenomics/adam into nested-variant-3