m2 wdl works with cram

[davidbenjamin]

Closes #4285.

@LeeTL1220 Here you go. Note the additional changes besides those mentioned in #4285. I'm going to head out before finding out whether tests pass. If they fail I will try to address tonight.

[LeeTL1220]

@davidbenjamin Feel free to merge if tests pass.

[codecov-io]

Codecov Report

Merging #4297 into master will decrease coverage by 0.005%.
The diff coverage is n/a.

@@              Coverage Diff               @@
##              master    #4297       +/-   ##
==============================================
- Coverage     79.095%   79.09%   -0.005%     
+ Complexity     16615    16611        -4     
==============================================
  Files           1049     1049               
  Lines          59580    59580               
  Branches        9730     9730               
==============================================
- Hits           47125    47122        -3     
- Misses          8679     8680        +1     
- Partials        3776     3778        +2

Impacted Files	Coverage Δ	Complexity Δ
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...park/sv/discovery/alignment/AlignmentInterval.java	89.272% <0%> (-0.766%)	73% <0%> (-2%)
...e/hellbender/engine/spark/SparkContextFactory.java	73.973% <0%> (+2.74%)	11% <0%> (ø)	⬇️