[ADAM-582] Eliminate .get on option in FragmentCoverter. #1091
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Resolves bigdatagenomics#582. In the FragmentConverter, we had code that called .get on an optional ReferenceRegion. If a NucleotideContigFragment didn't have a contig associated with it, then we would call .get on the empty option, which would throw an error. This commit changes that code to call map on the Option[ReferenceRegion], and then changes the usage of that method so that it is called in a flatMap. Additionally, I've added a test to cover this case.
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+1 |
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Test PASSed. |
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Resolves #582. In the FragmentConverter, we had code that called .get on an optional ReferenceRegion. If a NucleotideContigFragment didn't have a contig associated with it, then we would call .get on the empty option, which would throw an error. This commit changes that code to call map on the Option[ReferenceRegion], and then changes the usage of that method so that it is called in a flatMap. Additionally, I've added a test to cover this case.