added ReferenceMapping for Genotype

added filterByOverlappingRegion for GenotypeRDDFunctions
refactor RDD loading; explicitly load alignments

There’s really not a case where we are loading a generic Parquet file of
SpecificRecords whose type we don’t have a strong requirement about;
on the other hand, there is a case where we know what type we want
(AlignmentRecord) but don’t know which code path to read it in via (sam,
bam, ifq, fq, parquet, …).

Here I’ve made the caller explicitly specify if it wants
AlignmentRecords (which it was previously doing by labeling the return
value), but wants to benefit from the smarts around file-extension
inference.

Parquet reads with a known type can still go through one place so that
we can continue to benefit from that code not needing to be duplicated,
by only relying on SpecificRecord.
Merge pull request #468 from ryan-williams/loading

refactor RDD loading; explicitly load alignments
Merge pull request #470 from erictu/master

added ReferenceMapping for Genotype, filterByOverlappingRegion for GenotypeRDDFunctions
Reverting README.md back to 17d1d4d7d2e302c5dc4b9ba8e09e24fb9b8a48fb.
[ADAM-476] Adding 'childLocators' to FileLocator

Updated the FileLocator trait to include a childLocators method, which
implements the ability to scan the children of a locator (in addition to
finding the parent).  This will be required for the AvroMultiParquetRDD
we're planning to introduce.  Unfortunately (see the comments) this
isn't possible to implement in HTTPFileLocator without additional
assumptions.

Also filled in the implementation of some missing methods in
HTTPFileLocator in this commit, and added comments to FileLocator
overall.
[ADAM-477] Adding HDFSFileLocator implementation

HDFSFileLocator implements the FileLocator API, but uses the Hadoop
interface to find files in an HDFS system.

Includes the InputStreamByteAccess implementation, which is used
internally.
[ADAM-463] Added AvroMultiParquetRDD

AvroMultiParquetRDD takes a FileLocator which indicates the _parent_
directory (in HDFS, or S3) of a set of parquet files, and which loads
_all_ row groups from all the parquet files that are immediate children
of that FileLocator.

(Here, "children" is defined w/r/t the childLocators method
implementation in the corresponding FileLocator.)

(Joint work with Carl Yeksigian.)