Refactor CRAM package code

[cmnbroad]

Notes for the PR:

• This does not change the default encoding strategy used by htsjdk
• The CRAM layer API is changed considerably. Most known clients will only require minor changes (Disq, IGV, and Hadoop-BAM). Some (GATK and Picard) will require none.
• New abstractions/classes (Container, Slice, CompressionHeader, etc) are immutable wherever possible, with 2 constructors (one to read from a stream, and one to create the object from component classes).
• Includes read support for embedded reference
• No longer requires a reference to be provided on read (except when one is actually need to resolve CRAM records to SAMRecords)
• The tag handling code, digest code, and I/O layer are largely unchanged in this PR (though much of that has been moved to new classes). Only minimal changes were made to the upper integration layer between the CRAM package and the SAM reader and writer factories.
• There are many new tests, and the test suite run time is increased.
• CRAMRecordReadFeatures and mate resolution tests and code are still being added.

Reviewer	Focus area	Complete
@lbergelson	htsjdk.samtools.cram.structure.{Container, Slice, SliceBlocks, SliceBlocksReadStreams, SliceBlocksWriteStreams, CompressionHeaderEncodingMap}	- [ ]
@droazen	ContainerFactory, CompressionHeaderFactory, SliceFactory, Huffman codec, indexing test coverage	- [ ]
@jamesemery	htsjdk.samtools.cram.encoding.{CRAMRecord, CramRecordReader, CramRecordWriter, CRAMRecordReadFeatures}	- [ ]

Partial list of issue fixes (more to come s they are verified): https://github.com/samtools/htsjdk/issues/1422 https://github.com/samtools/htsjdk/issues/1394 https://github.com/samtools/htsjdk/issues/1379 https://github.com/samtools/htsjdk/issues/1367 https://github.com/samtools/htsjdk/issues/1343 https://github.com/samtools/htsjdk/issues/1307 https://github.com/samtools/htsjdk/issues/1301 https://github.com/samtools/htsjdk/issues/1187 https://github.com/samtools/htsjdk/issues/1183 https://github.com/samtools/htsjdk/issues/1088

[codecov-io]

Codecov Report

Merging #1440 into master will increase coverage by 0.743%. The diff coverage is 82.635%.

@@               Coverage Diff               @@
##              master     #1440       +/-   ##
===============================================
+ Coverage     68.381%   69.124%   +0.743%     
- Complexity      8631      8710       +79     
===============================================
  Files            591       587        -4     
  Lines          34966     34535      -431     
  Branches        5838      5766       -72     
===============================================
- Hits           23910     23872       -38     
+ Misses          8793      8399      -394     
- Partials        2263      2264        +1

Impacted Files	Coverage Δ	Complexity Δ
...samtools/cram/encoding/core/GammaIntegerCodec.java	95.238% <ø> (ø)	6 <0> (ø)	:arrow_down:
.../samtools/cram/encoding/readfeatures/SoftClip.java	50% <ø> (-4.545%)	6 <0> (-1)
...s/cram/encoding/readfeatures/BaseQualityScore.java	0% <ø> (ø)	0 <0> (ø)	:arrow_down:
.../java/htsjdk/samtools/cram/digest/Crc32Hasher.java	73.684% <ø> (ø)	4 <0> (ø)	:arrow_down:
...s/cram/encoding/external/ExternalIntegerCodec.java	83.333% <ø> (ø)	3 <0> (ø)	:arrow_down:
...cram/encoding/core/SubexponentialIntegerCodec.java	96.154% <ø> (ø)	7 <0> (ø)	:arrow_down:
...dk/samtools/cram/structure/SubstitutionMatrix.java	88.189% <ø> (ø)	25 <0> (ø)	:arrow_down:
...samtools/cram/encoding/readfeatures/Insertion.java	50% <ø> (ø)	5 <0> (-1)	:arrow_down:
...va/htsjdk/samtools/cram/digest/ContentDigests.java	53.465% <ø> (+2.998%)	9 <0> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/SAMRecord.java	68.323% <ø> (ø)	297 <0> (ø)	:arrow_down:
... and 172 more