Shard readGroupSets using the associated referenceSet. #64
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| public static Iterable<Reference> getReferences(String referenceSetId, GenomicsFactory.OfflineAuth auth) | ||
| throws IOException, GeneralSecurityException { | ||
| Genomics genomics = auth.getGenomics(auth.getDefaultFactory()); | ||
| Iterable<Reference> references = Paginator.References.create( |
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Local variable seems unnecessary here.
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Thanks for the feedback @calbach. PTAL I switched to Coverage Buckets for read group set sharding. Its much better to use something available for all read group sets. I left the getReferenceId and getReference methods in the utility class since they're generally useful. |
| public static List<CoverageBucket> getCoverageBuckets(String readGroupSetId, GenomicsFactory.OfflineAuth auth) | ||
| throws IOException, GeneralSecurityException { | ||
| Genomics genomics = auth.getGenomics(auth.getDefaultFactory()); | ||
| // Not using a Paginator here because requests of this form return one result per |
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I don't agree that this is a safe assumption. If there is already a paginator I would strongly prefer it were used. Otherwise, you should at least throw an exception if nextPageToken is set.
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There is no Paginator for that method. I added the exception.
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LGTM |
| genomics.readgroupsets().coveragebuckets().list(readGroupSetId).execute(); | ||
| // Requests of this form return one result per reference name, so therefore many fewer than | ||
| // the default page size, but verify that the assumption holds true. | ||
| if(null != response.getNextPageToken()) { |
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Strings.isNullOrEmpty() would probably be safer
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LGTM
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Shard readGroupSets using the associated referenceSet.
Take a look at deflaux/dataflow-java@33f0cff so see how this change could be used downstream. (but I plan to refactor that refactor; it needs a bit more work)