Count the number of warnings and errors during SAM file validation

[ronlevine]

Description

Count the number of warnings and errors so Picard's ValidateSamFile can determine the appropriate exit code described in broadinstitute/picard#794.

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)

[ronlevine]

@tfenne Please review.

[codecov-io]

Codecov Report

Merging #855 into master will increase coverage by 0.018%.
The diff coverage is 66.667%.

@@              Coverage Diff               @@
##              master     #855       +/-   ##
==============================================
+ Coverage     64.922%   64.94%   +0.018%     
- Complexity      7203     7209        +6     
==============================================
  Files            527      527               
  Lines          31789    31800       +11     
  Branches        5425     5426        +1     
==============================================
+ Hits           20638    20651       +13     
  Misses          9017     9017               
+ Partials        2134     2132        -2

Impacted Files	Coverage Δ	Complexity Δ
...rc/main/java/htsjdk/samtools/SamFileValidator.java	85.132% <66.667%> (-0.336%)	73 <2> (+3)
...dk/samtools/seekablestream/SeekableHTTPStream.java	56.061% <0%> (+1.515%)	10% <0%> (+1%)	⬆️
...a/htsjdk/samtools/cram/encoding/rans/Decoding.java	85.714% <0%> (+3.571%)	12% <0%> (+1%)	⬆️
...samtools/util/AsyncBlockCompressedInputStream.java	76% <0%> (+4%)	13% <0%> (+1%)	⬆️

[ronlevine]

@yfarjoun Could you take a look?

[yfarjoun]

tiny request 👍 after that.

[yfarjoun]

can you protect this against a new Severity level?

[ronlevine]

Changed to a switch statement that handles each known error type and throws a SAMException if it's an unknown error.

[ronlevine]

@yfarjoun Squashing and merging once tests pass if that's fine with you.

[yfarjoun]

yup. go ahead.