Support VCF v4.3 (read only).

[cmnbroad]

Read-only support for VCF v4.3:

• ALT header lines are now modeled with a new VCFSimpleHeaderLine-derived VCAltHeaderLine class (previously these were modeled directly with VCFSimpleHeaderLine objects). SAMPLE, META and PEDIGREE header lines are also modeled with VCFSimpleHeaderLine-derived classes (previously these would have been tolerated on read, even for v4.x files, and modeled as VCFHeaderLine). VCFHeaderLine does not allow attribute queries.
• Supports reading files with UTF8 character encoding (v4.3).
• Supports percent-encoded values (v43).
• Adds a VCFHeaderVersion field to VCF header; once a VCFHeader is established as v4.3, it cannot be transitioned to any other version.
• Merging a v4.3 header with other headers is only allowed if all headers being merged are v4.3.
• VCFWriter throws on any attempt to write out a version v43 header.
• Except for the class change of ALT header lines, these changes should be invisible to existing callers.

[codecov-io]

Codecov Report

Merging #1359 into master will increase coverage by 0.096%. The diff coverage is 94.161%.

@@               Coverage Diff               @@
##              master     #1359       +/-   ##
===============================================
+ Coverage     67.863%   67.959%   +0.096%     
- Complexity      8289      8326       +37     
===============================================
  Files            563       570        +7     
  Lines          33718     33797       +79     
  Branches        5659      5660        +1     
===============================================
+ Hits           22882     22968       +86     
+ Misses          8656      8649        -7     
  Partials        2180      2180

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/htsjdk/variant/vcf/VCFEncoder.java	86.935% <ø> (ø)	72 <0> (ø)	:arrow_down:
src/main/java/htsjdk/variant/vcf/VCFCodec.java	77.273% <0%> (ø)	17 <0> (+1)	:arrow_up:
...n/java/htsjdk/variant/vcf/VCFSampleHeaderLine.java	100% <100%> (ø)	1 <1> (?)
src/main/java/htsjdk/variant/vcf/VCFHeader.java	90.058% <100%> (+1.243%)	76 <8> (+10)	:arrow_up:
...main/java/htsjdk/variant/vcf/VCFHeaderVersion.java	71.875% <100%> (+7.986%)	13 <2> (-5)	:arrow_down:
...va/htsjdk/variant/vcf/VCFHeaderLineTranslator.java	93.976% <100%> (+1.383%)	3 <1> (ø)	:arrow_down:
src/main/java/htsjdk/variant/vcf/VCFConstants.java	87.5% <100%> (+87.5%)	1 <0> (+1)	:arrow_up:
src/main/java/htsjdk/variant/vcf/VCFUtils.java	44.444% <100%> (+6.391%)	17 <6> (+6)	:arrow_up:
...ava/htsjdk/variant/vcf/VCFStandardHeaderLines.java	77.632% <100%> (+1.243%)	13 <6> (+2)	:arrow_up:
...main/java/htsjdk/variant/vcf/VCFAltHeaderLine.java	100% <100%> (ø)	2 <2> (?)
... and 30 more

[cmnbroad]

Back to you @lbergelson. I relaxed the percent encoding to be more permissive and only transfor encodings if the % is followed by two legitimate hex-digit values, otherwise the raw characters are passed through untranslated.

[droazen]

@lbergelson Waiting for a final 👍 from you on this one.