fixed a GGA mode bug where added alleles' cigars had soft clips

[davidbenjamin]

Closes #6037

@ldgauthier This fixes the Karlsson group's bug with long insertions.

@cwhelan This also fixes Giulio's bug.

[codecov]

Codecov Report

Merging #6047 into master will decrease coverage by 61.627%.
The diff coverage is 50%.

@@               Coverage Diff                @@
##              master     #6047        +/-   ##
================================================
- Coverage     80.376%   18.749%   -61.627%     
+ Complexity     31022      4627     -26395     
================================================
  Files           2011      1258       -753     
  Lines         150967     73151     -77816     
  Branches       16134     11631      -4503     
================================================
- Hits          121341     13715    -107626     
- Misses         24157     57390     +33233     
+ Partials        5469      2046      -3423

Impacted Files	Coverage Δ	Complexity Δ
...der/tools/walkers/haplotypecaller/graphs/Path.java	50.877% <0%> (-45.614%)	8 <0> (-16)
...kers/haplotypecaller/AssemblyBasedCallerUtils.java	34.593% <0%> (-55.233%)	41 <0> (-90)
...oadinstitute/hellbender/utils/read/CigarUtils.java	30.806% <100%> (-63.507%)	27 <0> (-72)
...pecaller/readthreading/ReadThreadingAssembler.java	52.479% <100%> (-13.636%)	29 <0> (-20)
...hellbender/engine/spark/IntervalWalkerContext.java	0% <0%> (-100%)	0% <0%> (-5%)
...ls/walkers/mutect/filtering/BaseQualityFilter.java	0% <0%> (-100%)	0% <0%> (-6%)
...nder/tools/readersplitters/SampleNameSplitter.java	0% <0%> (-100%)	0% <0%> (-2%)
...nder/tools/spark/pipelines/CountVariantsSpark.java	0% <0%> (-100%)	0% <0%> (-4%)
...broadinstitute/hellbender/utils/svd/SimpleSVD.java	0% <0%> (-100%)	0% <0%> (-5%)
...lbender/tools/walkers/mutect/clustering/Datum.java	0% <0%> (-100%)	0% <0%> (-7%)
... and 1845 more

[ldgauthier]

Thanks for the fix!