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 with latest upstream changes + local changes to write out ADAMVCF files locally. Have not tested on cluster yet.
Fill out contig data in variant conversion if dictionary is available.

Conflicts:
	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/rich/RichADAMVariant.scala
Expanded variant schema, including setting some variant fields
More comprehensive VCF conversion, including INFO fields