Documentation cleanup and minor refactor on the consensus package. #1055
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Test PASSed. |
| * @note This method can only generate a single consensus from a read. Reads | ||
| * with more than one INDEL operator are ignored. | ||
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| * @param sequence Read sequence. |
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@param comments don't need to be full sentences
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Left some comments regarding doc comment style. The style I suggest is more in line with other major Java code bases, such as Apache Commons and Google Guava. It does not match the style of comments already in the ADAM code base, so perhaps the general open source principle of matching the style already in the code should win. |
| @@ -68,7 +76,16 @@ class ConsensusGeneratorFromReads extends ConsensusGenerator { | |||
| } | |||
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| /** | |||
| * Generates concensus sequences from reads with indels. | |||
| * Generates concensus sequences from reads with INDELs. | |||
* Moved `org.bdgenomics.adam.models.Concensus` to `org.bdgenomics.adam.algorithms.consensus.Consensus`. * Made all classes in `org.bdgenomics.adam.algorithms.consensus` package private to `org.bdgenomics.adam`, along with `IndelTable` and `NormalizationUtils`. * Fleshed out documentation for all classes and methods in `org.bdgenomics.adam.algorithms.consensus.Consensus`. * Refactored `Consensus` method to use `ReferenceRegion` instead of `start`/`end` to check overlap bounds. This led to the discovery of an off by one error in `ConsensusSuite`, which was then fixed.
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Addressed typos and rebased. |
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Test PASSed. |
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Thank you, @fnothaft! |
org.bdgenomics.adam.models.Concensustoorg.bdgenomics.adam.algorithms.consensus.Consensus.org.bdgenomics.adam.algorithms.consensuspackage private toorg.bdgenomics.adam, along withIndelTableandNormalizationUtils.org.bdgenomics.adam.algorithms.consensus.Consensus.Consensusmethod to useReferenceRegioninstead ofstart/endto check overlap bounds. This led to the discovery of an off by one error inConsensusSuite, which was then fixed.