Gff3 Tribble Codec

[kachulis]

Adds a Gff3 tribble codec for reading gff3 files. Based on specification defined at https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md. This PR focuses on implementing the capability to read this format; it does not implement any ontological validation of feature types or allowed relationships between features of different types. It is thus only a partial implementation of the specification.

[codecov-io]

Codecov Report

Merging #1439 into master will increase coverage by 0.172%. The diff coverage is 76.515%.

@@               Coverage Diff               @@
##              master     #1439       +/-   ##
===============================================
+ Coverage     68.343%   68.516%   +0.172%     
- Complexity      8489      8613      +124     
===============================================
  Files            583       589        +6     
  Lines          34391     34843      +452     
  Branches        5729      5808       +79     
===============================================
+ Hits           23504     23873      +369     
- Misses          8668      8715       +47     
- Partials        2219      2255       +36

Impacted Files	Coverage Δ	Complexity Δ
...main/java/htsjdk/samtools/util/FileExtensions.java	80% <100%> (+5%)	1 <0> (ø)	:arrow_down:
src/main/java/htsjdk/tribble/gff/Gff3Feature.java	58.333% <58.333%> (ø)	7 <7> (?)
src/main/java/htsjdk/tribble/gff/Gff3BaseData.java	72.917% <72.917%> (ø)	15 <15> (?)
src/main/java/htsjdk/tribble/gff/Gff3Codec.java	76.596% <76.596%> (ø)	48 <48> (?)
.../main/java/htsjdk/tribble/gff/Gff3FeatureImpl.java	78.462% <78.462%> (ø)	38 <38> (?)
...c/main/java/htsjdk/tribble/gff/SequenceRegion.java	82.353% <82.353%> (ø)	7 <7> (?)
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java	80.952% <0%> (-9.524%)	3% <0%> (-1%)
...in/java/htsjdk/samtools/SAMSequenceDictionary.java	73.239% <0%> (-2.113%)	45% <0%> (-1%)
src/main/java/htsjdk/samtools/util/Interval.java	66.667% <0%> (-1.667%)	26% <0%> (-3%)
...c/main/java/htsjdk/samtools/SAMFileWriterImpl.java	80.822% <0%> (-1.123%)	25% <0%> (ø)
... and 14 more

[kachulis]

@lbergelson back to you. While I was addressing your comments, I realized that I was depending on parent features being before child features in the input files, which is not at all guaranteed. This is fixed now (with added tests), but means the parent maps, which used to be immutable, are now mutable, with public modifying methods.

[kachulis]

@lbergelson a few changes since you approved, these resulted from getting some full scale use cases working:

1) clear activeParentIDs in Gff3Codec::prepareToFlushFeatures(). This is needed to avoid memory leak and massive garbage collection problems when using (for example) a full scale human annotation file.

2) clear all maps and queues in Gff3Codec::close. This is needed to avoid parsed, but unreturned features from persisting through close, and later being returned incorrectly when the same codec is used to read from a potentially completely different stream.

3) (minor) adjusted directive regex to allow for variable number of spaces

At this point, my use cases are working, and I am content with where this is. I don't have the authorization to merge this, so feel free to go ahead and merge if you don't have any issues with the additional changes.