ReadsPipelineSpark fails with "Interval not within the bounds of a contig"

[tomwhite]

Fixes #5644.

The issue was that different sequence dictionaries were being used.

[codecov-io]

Codecov Report

Merging #5645 into master will decrease coverage by 0.594%.
The diff coverage is 0%.

@@               Coverage Diff               @@
##              master     #5645       +/-   ##
===============================================
- Coverage     87.035%   86.441%   -0.594%     
- Complexity     31726     31896      +170     
===============================================
  Files           1943      1943               
  Lines         146193    148531     +2338     
  Branches       16141     16607      +466     
===============================================
+ Hits          127239    128391     +1152     
- Misses         13067     14170     +1103     
- Partials        5887      5970       +83

Impacted Files	Coverage Δ	Complexity Δ
...nder/tools/spark/pipelines/ReadsPipelineSpark.java	90.741% <0%> (ø)	13 <0> (ø)	⬇️
...ols/funcotator/FuncotatorDataSourceDownloader.java	37.008% <0%> (-29.189%)	9% <0%> (-5%)
...llbender/utils/reference/FastaReferenceWriter.java	64.593% <0%> (-27.872%)	48% <0%> (-3%)
...ces/gencode/GencodeFuncotationFactoryUnitTest.java	68.254% <0%> (-25.784%)	35% <0%> (-32%)
.../utils/reference/FastaReferenceWriterUnitTest.java	62.443% <0%> (-22.696%)	33% <0%> (-37%)
...ellbender/tools/walkers/vqsr/CNNScoreVariants.java	58.387% <0%> (-22.057%)	33% <0%> (-12%)
.../walkers/vqsr/CNNScoreVariantsIntegrationTest.java	78.534% <0%> (-21.466%)	8% <0%> (-5%)
...ownsampling/ReadsDownsamplingIteratorUnitTest.java	51.724% <0%> (-20.407%)	7% <0%> (-4%)
...ender/utils/downsampling/ReservoirDownsampler.java	86.301% <0%> (-13.699%)	33% <0%> (+6%)
...ils/downsampling/ReservoirDownsamplerUnitTest.java	77.273% <0%> (-10.356%)	13% <0%> (ø)
... and 18 more

[lbergelson]

Good catch! 👍