The existing code was throwing a NPE when using a CRAMFileReader for …

[skashin]

…InputResource.Type.PATH

Description

Please explain the changes you made here.
Explain the motivation for making this change. What existing problem does the pull request solve?

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 #879 into master will increase coverage by 0.007%.
The diff coverage is 67.241%.

@@               Coverage Diff               @@
##              master      #879       +/-   ##
===============================================
+ Coverage     65.006%   65.013%   +0.007%     
- Complexity      7229      7234        +5     
===============================================
  Files            528       528               
  Lines          31894     31895        +1     
  Branches        5444      5443        -1     
===============================================
+ Hits           20733     20736        +3     
- Misses          9013      9015        +2     
+ Partials        2148      2144        -4

Impacted Files	Coverage Δ	Complexity Δ
...rc/main/java/htsjdk/samtools/SamReaderFactory.java	61.809% <67.241%> (-1.456%)	7 <0> (ø)
...dk/samtools/seekablestream/SeekableFileStream.java	61.905% <0%> (-7.143%)	13% <0%> (-1%)
...sjdk/samtools/util/Md5CalculatingOutputStream.java	76.923% <0%> (-2.564%)	9% <0%> (ø)
.../main/java/htsjdk/tribble/index/AbstractIndex.java	52.91% <0%> (+1.331%)	31% <0%> (+1%)	⬆️
...c/main/java/htsjdk/samtools/fastq/FastqReader.java	82.432% <0%> (+1.351%)	26% <0%> (+2%)	⬆️
src/main/java/htsjdk/samtools/util/StringUtil.java	67.692% <0%> (+1.538%)	67% <0%> (+2%)	⬆️
...in/java/htsjdk/tribble/index/tabix/TabixIndex.java	78.788% <0%> (+1.679%)	39% <0%> (+1%)	⬆️

[yfarjoun]

Thanks for this.

this needs to be protected against future changes...can you please convert the list of if statements to a switch that includes a default case that will throw an exception? that should make things more clear when they break....

[skashin]

No problem, I switched away from the if statements

[yfarjoun]

👍

[yfarjoun]

much better, thanks.

[yfarjoun]

I guess you could revert the revert in a new branch and run the tests....or submit a PR and have travis test for you.

[skashin]

I ran "./gradlew test", and that built successfully.
What exactly did you mean by "somehow it broke the build"?

[yfarjoun]

@lbergelson can you help here?