fix bug causing error finding ref base for imprecise deletions

[cwhelan]

This PR fixes a critical error that was causing an "invalid interval" exception to be thrown while calling imprecise deletion intervals. The problem was a mismatch between the sequence dictionary in the reference and the read metadata's contig ID - contig name mapping. I've modified the code to always use the read metadata when translating the contig ID in EvidenceTargetLink intervals into contig names.

[cwhelan]

@tedsharpe this should fix your error on NA12878; I just ran that sample through without hitting an exception with this code change. Want to take a look at the changes?

[tedsharpe]

Looks good.

[codecov-io]

Codecov Report

Merging #3671 into master will increase coverage by 0.035%.
The diff coverage is 91.667%.

@@               Coverage Diff               @@
##              master     #3671       +/-   ##
===============================================
+ Coverage     79.266%   79.301%   +0.035%     
- Complexity     17397     17412       +15     
===============================================
  Files           1144      1144               
  Lines          62931     63048      +117     
  Branches        9551      9580       +29     
===============================================
+ Hits           49883     49998      +115     
+ Misses          9241      9233        -8     
- Partials        3807      3817       +10

Impacted Files	Coverage Δ	Complexity Δ
...s/spark/sv/discovery/AnnotatedVariantProducer.java	74.79% <100%> (ø)	23 <1> (ø)	⬇️
...ute/hellbender/tools/spark/sv/utils/SVContext.java	76.033% <100%> (ø)	21 <0> (ø)	⬇️
...lbender/tools/spark/sv/discovery/SimpleSVType.java	86.567% <100%> (ø)	2 <0> (ø)	⬇️
.../DiscoverVariantsFromContigAlignmentsSAMSpark.java	93.478% <80%> (-1.027%)	24 <5> (+1)
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	79.87% <0%> (+1.299%)	39% <0%> (ø)	⬇️
.../hellbender/tools/genomicsdb/GenomicsDBImport.java	81.432% <0%> (+7.103%)	68% <0%> (+14%)	⬆️