Recognize MEI DELs with ALT format <DEL:ME> in SVAnnotate

[epiercehoffman]

Updates

Some GATK-SV VCFs contain MEI deletions with ALT in the format DEL:ME:ALU or DEL:ME. This change will allow SVAnnotate to recognize and annotate those records as deletions.

Testing

• Added unit test with MEI DEL
• Ran all unit and integration tests for SVAnnotate

[codecov]

Codecov Report

Merging #8125 (3eb4c98) into master (84ade40) will increase coverage by 40.209%.
The diff coverage is 100.000%.

Additional details and impacted files

@@               Coverage Diff                @@
##              master     #8125        +/-   ##
================================================
+ Coverage     46.436%   86.645%   +40.209%     
- Complexity     26473     38952     +12479     
================================================
  Files           2336      2336                
  Lines         182709    182710         +1     
  Branches       20060     20059         -1     
================================================
+ Hits           84843    158309     +73466     
+ Misses         91960     17366     -74594     
- Partials        5906      7035      +1129     

Impacted Files	Coverage Δ
.../hellbender/tools/walkers/sv/SVAnnotateEngine.java	89.781% <100.000%> (-0.074%)	⬇️
...der/tools/walkers/sv/SVAnnotateEngineUnitTest.java	96.552% <100.000%> (+94.226%)	⬆️
...roadinstitute/hellbender/tools/LocalAssembler.java	67.425% <0.000%> (+0.073%)	⬆️
...r/tools/walkers/varianteval/VariantEvalEngine.java	84.040% <0.000%> (+0.249%)	⬆️
...itute/hellbender/utils/report/GATKReportTable.java	70.370% <0.000%> (+0.370%)	⬆️
...stitute/hellbender/utils/clipping/ReadClipper.java	74.138% <0.000%> (+0.575%)	⬆️
...lkers/annotator/allelespecific/AS_RankSumTest.java	87.195% <0.000%> (+0.610%)	⬆️
...kers/variantutils/PosteriorProbabilitiesUtils.java	81.875% <0.000%> (+0.625%)	⬆️
...stitute/hellbender/cmdline/CommandLineProgram.java	84.516% <0.000%> (+0.645%)	⬆️
...nstitute/hellbender/utils/read/AlignmentUtils.java	81.716% <0.000%> (+0.677%)	⬆️
... and 826 more

[mwalker174]

Great!