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bigdatagenomics / bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
Apache License 2.0
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Refactor AlignmentRecord, RecordGroup, and ProcessingStep #175

Closed heuermh closed 5 years ago

heuermh commented 5 years ago

Fixes #126, #130, #155

Cherry-picks commit 060015e481dbbeee7a7d123217ba7c4656f0578e from pull request #143 and then continues to refactor AlignmentRecord, RecordGroup, and ProcessingStep to more closely align with the SAM specification.

Specifically, RecordGroup → ReadGroup RecordGroup.name → ReadGroup.id added ReadGroup.platformModel RecordGroup.sample → ReadGroup.sampleId AlignmentRecord.oldPosition → AlignmentRecord.originalStart AlignmentRecord.mapq → AlignmentRecord.mappingQuality AlignmentRecord.qual → AlignmentRecord.quality AlignmentRecord.oldCigar → AlignmentRecord.originalCigar AlignmentRecord.origQual → AlignmentRecord.originalQuality AlignmentRecord.recordGroupName → AlignmentRecord.readGroupId AlignmentRecord.recordGroupSample → AlignmentRecord.readGroupSampleId AlignmentRecord.inferredInsertSize → AlignmentRecord.insertSize Fragment.recordGroupName → Fragment.readGroupId Sample.sampleId → Sample.id

164 could also be applied here; I'd rather do it in a separate pull request as the downstream refactoring would be much more involved.

AmplabJenkins commented 5 years ago

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/187/ Test PASSed.