Fixed error in FilterIntervals logic when filtering on annotations with -XL.

[samuelklee]

Fixes a bug that I inadvertently introduced long ago in #5408. A method there originally assumed that the intervals to be filtered coincide with the annotated intervals when filtering on annotations, but this assumption can be violated when e.g. using -XL to further exclude intervals. This breaks the annotation-based filtering and will result in incorrectly retained/dropped intervals. Unfortunately, the integration test cases were not quite complete enough to catch this.

Fortunately, for typical data and parameters, the number of affected intervals is typically a very small percentage, especially in human (e.g., the default GC filters of [0.1, 0.9] affect <0.1% of 250bp bins); I only caught this when running on malaria data, since GC filtering has more impact there. I would also expect count-based filters to mitigate some of the effects (e.g., a bin with extreme GC that was erroneously retained when filtering on annotations might later be filtered because it has poor coverage). Downstream results are also all correct---they're just given for a slightly different set of intervals than would be expected.

This bug would affect users that made use of the blacklist_intervals_for_filter_intervals option in the gCNV WDLs, but my feeling is this functionality is not used that frequently.

@droazen I think this is a relatively minor bug, but it might be good to mention it in the release notes.

[gatk-bot]

Travis reported job failures from build 32589
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	openjdk11	32589.12	logs
integration	openjdk8	32589.2	logs

[samuelklee]

@mwalker174 quick one for you. Tried to do a bit of clean up in the parsing of optional inputs; there is still some duplication of code, but I think I'm OK with it. Sorry this went undetected for so long, but maybe that's a good thing!

[mwalker174]

Thanks for catching this. I don't believe this would have had a large impact on WGS. One suggestion, but otherwise looks good!

[samuelklee]

Thanks @mwalker174, will merge once tests pass.