Fixed typo on MAVEN_OPTS quotation mark
Merge pull request #471 from neurons/fix_readme

Fixed typo on MAVEN_OPTS quotation mark
Consolidate documentation into a single location in source.

This system uses `pandoc` to convert Markdown into PDF and HTML
for each release. These currents docs were taken from our Wiki
and README.
Merge pull request #474 from massie/docs

Consolidate documentation into a single location in source.
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
added ReferenceMapping for Genotype

added filterByOverlappingRegion for GenotypeRDDFunctions