New flagstat command. Upgrade to Parquet 1.2.5. Reference ID bugfix.

o Added a new flagstat command which write ADAM stats identically to samtools flagstat
o Upgraded to Parquet 1.2.5
o Fixed bug where the mate reference id was being written to the read reference id
o Created a new ADAMRecordField enum to help prevent typos in code with literal strings
o Added log4j.properties file to turn down logging in local mode
Typo
Updated README
Small changes to README
README cleanup
Update README
Fix mpileup command
Added read name, start, and end fields to pileup. Also, refactored Reads2Ref so that it does not try to create pileups for unmapped reads.
Merge pull request #13 from fnothaft/adam-pileup

Updated pileup/reads2ref with additional read name/start/end fields
Support marking duplicates including PE reads that cross chromosomes

This commit also:
o Adds a new operation, adamReadPairs(), to RDD[ADAMRecord] which
  groups the reads into ReadPair objects
o Adds new duplication metrics to the 'flagstat' command that show
  primary/secondary alignment, read/mate mapping and cross-chromosome
  duplicate reads
o Speed improvements (~10%) to the AvroSerialization class
o Adds a new class, ReferencePositionWithOrientation, which captures
  the read orientation as well as the position. Supports calculating
  the 5' position.
o Adds support for 5' position calculation to ReferencePosition class
o Removes the unused MatedReferencePosition class
o Fixes the default block size in adamSave() from 512mb to 128mb
o Adds phred score calculation to RichAdamRecord
Fixed a typo (RichAdamRecord -> RichADAMRecord)
Merge pull request #14 from tdanford/tdanford-richadamrecord-typo-fix

Fixed a typo (RichAdamRecord -> RichADAMRecord)
Allow BAM/SAM files as input to the 'transform' command.

This commit adds Hadoop-BAM back to ADAM and allows users to use BAM/SAM files as
input to the transform command.

Running e.g.

$ adam transform foo.bam foo.adam

will execute a simple file transform from BAM to ADAM formats.

Running e.g.

$ adam tranform -mark_duplicate_reads foo.bam foo.adam

will load the BAM file, mark duplicates and then save to the ADAM format.
Fix typo