Adding Yy as base in MdTag
Merge pull request #56 from arahuja/mdtag

Adding Yy as base in MdTag
Adding reads to rods transformation.
Merge pull request #36 from bigdatagenomics/reads-to-rods

Adding reads to rods transformation.
Parse read groups and create mapping from bam/sam header
Merge pull request #48 from arahuja/readgroupsmapping

Parse read groups and create mapping from bam/sam header
Added the "tags" command, and parsing for BAM attributes.

Added code (in Attribute and AttributeUtils) to parse attributes -- the optional fields at the end of a SAM record -- from the string which is stored in the ADAMRecord.

Updated the adam-cli project with a command, 'tags', that reads an ADAMRecord set and prints the total set of tags found in the set, along with the number of times each tag appears.
Added an ExportFastq command.

ExportFastq takes an ADAM / BAM / SAM file as input, and produces a collection of fastq files
for the single-ended and paired-end reads with those file(s).  Depending on the number of partitions,
it may produce multiple fastq files; these can then be concatenated as necessary.
Starting to write an 'unconvert' method in SAMRecordConverter
Working on unconverter, created Export command.
Fleshed out the initial, local version of BAMExport.
Adding TODO comments.
More TODOs.