Adding getPathToDataFile default method to FeatureCodec

[lbergelson]

• adding a new method FeatureCodec.getPathToDataFile()
  • This method allows a special class of codec where the files that they accept are a configuration file and the actual data is stored elsewhere.
  • The default implementation means that existing codecs do not need to be modified in any way
• modifying AbstractFeatureReader and it's subclasses to use getPathToDataFile
• downstream tools that implement their own FeatureReader subclasses may want to update them to be aware of getPathToDataFile if they want to understand these codecs

Checklist

• [ ] Code compiles correctly
• [ ] New tests covering changes and new functionality
• [ ] All tests passing
• [ ] Extended the README / documentation, if necessary
• [ ] Is not backward compatible (breaks binary or source compatibility)

[codecov-io]

Codecov Report

Merging #1223 into master will decrease coverage by 0.078%. The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #1223       +/-   ##
===============================================
- Coverage     69.016%   68.938%   -0.078%     
- Complexity      8066      8197      +131     
===============================================
  Files            539       539               
  Lines          32552     32973      +421     
  Branches        5488      5591      +103     
===============================================
+ Hits           22466     22731      +265     
- Misses          7890      8012      +122     
- Partials        2196      2230       +34

Impacted Files	Coverage Δ	Complexity Δ
...c/main/java/htsjdk/tribble/TabixFeatureReader.java	68.657% <100%> (ø)	8 <0> (ø)	:arrow_down:
src/main/java/htsjdk/tribble/FeatureCodec.java	50% <100%> (+50%)	1 <1> (+1)	:arrow_up:
...ain/java/htsjdk/tribble/AbstractFeatureReader.java	70.213% <100%> (+0.648%)	17 <2> (ø)	:arrow_down:
...sjdk/samtools/util/Md5CalculatingOutputStream.java	66.667% <0%> (-7.692%)	7% <0%> (-1%)
...huffman/codec/CanonicalHuffmanIntegerEncoding.java	78.846% <0%> (-6.868%)	20% <0%> (+10%)
...samtools/cram/encoding/readfeatures/Insertion.java	34.375% <0%> (-4.514%)	8% <0%> (+4%)
src/main/java/htsjdk/samtools/LinearIndex.java	56.818% <0%> (-3.182%)	20% <0%> (+10%)
.../samtools/cram/encoding/readfeatures/SoftClip.java	36.364% <0%> (-2.525%)	9% <0%> (+5%)
src/main/java/htsjdk/tribble/index/Block.java	57.692% <0%> (-2.308%)	12% <0%> (+6%)
.../samtools/cram/encoding/readfeatures/Deletion.java	36.667% <0%> (-2.222%)	8% <0%> (+4%)
... and 15 more

[lbergelson]

@jrobinso As a heads up, this touches FeatureCodec, but I believe it should have no effect on IGV.

[jrobinso]

@lbergelson thanks for the heads up, I agree I don't see any impact.