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.
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-439] Fix ADAM to account for BDG-FORMATS-35

Includes commit by @fnothaft: Fixed flipped index in indel realigner.

Fixes #439
Merge pull request #440 from laserson/ADAM-439

[ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings
[ADAM-461] Fix ReferenceRegion and ReferencePosition impl

This commit mainly does 3 things:

1. Fixes impl of `ReferenceRegion.width`.

2. Removes `Option`s from `ReferencePosition`.

3. Corrected impl of liftOver.  However, it now has different semantics: in all cases, the list of regions must be provided in genome order.

4. Simplifies structure of case classes.

Fixes #461.
Merge pull request #469 from laserson/ADAM-461

[ADAM-461] Fix ReferenceRegion and ReferencePosition impl
[ADAM-486] Add port option to viz command.
Merge pull request #487 from fnothaft/unhardcode-viz

[ADAM-486] Add port option to viz command.
[ADAM-480] Switch assembly to single goal.
Merge pull request #481 from fnothaft/run-assembly-once

[ADAM-480] Switch assembly to single goal.
Fix foreach block for vcf ingest
Documentation cleanup and style improvements
Merge pull request #492 from massie/doc-cleanup

Documentation cleanup and style improvements