Add LiftOver constructor that takes an input stream

[kevinpetersavage]

Desrciption

Add LiftOver constructor that takes an input stream. This is so that it can be used in situations where the config is not on a file system. In my case it is on AWS S3.

Checklist

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

[codecov-io]

Codecov Report

Merging #1412 into master will increase coverage by 0.004%. The diff coverage is 58.824%.

@@               Coverage Diff               @@
##              master     #1412       +/-   ##
===============================================
+ Coverage     68.115%   68.118%   +0.004%     
- Complexity      8375      8378        +3     
===============================================
  Files            573       573               
  Lines          33978     33982        +4     
  Branches        5668      5668               
===============================================
+ Hits           23144     23148        +4     
  Misses          8644      8644               
  Partials        2190      2190

Impacted Files	Coverage Δ	Complexity Δ
...c/main/java/htsjdk/samtools/liftover/LiftOver.java	82.857% <100%> (+0.375%)	31 <2> (+2)	:arrow_up:
src/main/java/htsjdk/samtools/liftover/Chain.java	66.667% <36.364%> (+0.177%)	23 <1> (+1)	:arrow_up:

[kevinpetersavage]

@lbergelson thanks for the really good feedback, definitely improved the code!