Address classes with lower than ideal coverage

[fnothaft]

Now that we have easy-to-browse cover reports (#1404), let's do a deep dive and find out what code is not covered sufficiently. Would anyone be interested in helping? Perhaps we can split this effort up and divide-and-conquer?

[heuermh]

+1

[fnothaft]

Target is minimum 70% coverage per file.

• BQSR is uncovered, will be fixed as part of Performance tune-up in BQSR #1358
• Improve unit test coverage for NucleotideContigFragmentRDD, Improve unit test coverage for NucleotideContigFragmentRDD #1413
• Remove uncovered/unused Smith-Waterman code, Improve unit test coverage for NucleotideContigFragmentRDD #1413
• Write unittests for ParquetFileTraversable, Write unit tests for ParquetFileTraversable #1415
• Add tests across the CLI, Write unit tests for CLI #1416
• Improved INDEL realignment coverage in INDEL realigner cleanup #1412
• Improve JavaADAMContext coverage as WIP Python API #1387
• Delete low coverage RichVariant and DecadentRead classes as part of the Clean up Rich records #577 rich package refactor
• @heuermh sez he has a PR that cleans up some of the SaveArgs issues and which may improve coverage in the VCF save methods in GenotypeRDD -> Replace ADAM2Vcf and Vcf2ADAM commands with TransformGenotypes and TransformVariants #1327
• Delete unused/uncovered Projection.apply methods as Clean up possibly unused methods in Projection #1417
• Improve coverage of Feature encode/decode as Improve unit test coverage of Feature parser/encoder helper #1418
• Add coverage to BED12 read/write path as Add unit test coverage for BED12 parser and writer #1579

[heuermh]

Closing as WontFix