Fixing issue in ShiftFasta where the intervals aren't written

[meganshand]

@ahaessly Could you please take a look at this? I'd appreciate it if you would also look at the expected output and make sure those intervals make sense since I don't think that aspect of the code was previously tested and I want to be sure there are no off by one style errors.

[codecov]

Codecov Report

Merging #8070 (52a2d64) into master (9321181) will increase coverage by 34.106%.
The diff coverage is 100.000%.

Additional details and impacted files

@@               Coverage Diff                @@
##              master     #8070        +/-   ##
================================================
+ Coverage     52.542%   86.649%   +34.106%     
- Complexity     29595     38934      +9339     
================================================
  Files           2334      2334                
  Lines         182619    182632        +13     
  Branches       20048     20049         +1     
================================================
+ Hits           95952    158248     +62296     
+ Misses         80602     17351     -63251     
- Partials        6065      7033       +968     

Impacted Files	Coverage Δ
...ute/hellbender/tools/walkers/fasta/ShiftFasta.java	75.758% <100.000%> (+17.172%)	⬆️
...tools/walkers/fasta/ShiftFastaIntegrationTest.java	100.000% <100.000%> (ø)
...nder/utils/runtime/StreamingProcessController.java	66.818% <0.000%> (-0.455%)	⬇️
...roadinstitute/hellbender/tools/LocalAssembler.java	67.425% <0.000%> (+0.073%)	⬆️
...roadinstitute/hellbender/utils/read/ReadUtils.java	82.278% <0.000%> (+0.316%)	⬆️
...stitute/hellbender/cmdline/CommandLineProgram.java	84.516% <0.000%> (+0.645%)	⬆️
...lyBasedSVDiscoveryTestDataProviderForSimpleSV.java	100.000% <0.000%> (+0.894%)	⬆️
.../main/java/org/broadinstitute/hellbender/Main.java	72.685% <0.000%> (+1.389%)	⬆️
...llbender/engine/filters/SoftClippedReadFilter.java	94.286% <0.000%> (+2.857%)	⬆️
...VDiscoveryTestDataProviderForBreakEndVariants.java	100.000% <0.000%> (+3.279%)	⬆️
... and 589 more

[ahaessly]

👍