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Storage-MongoDB 2 steps loading #288
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Duplicated variants in Stage are not inserted in variants, but then set as not new variants for the study.
Use query ID = chr:pos:ref:alt instead of REGION, REFERENCE, ALTERNATE The previous version can return wrong results if in that region there is a variant with the same REF and ALT.
Avoid leave documents in stage collection setStatus RUNNING merge setStatus DONE clean stage update indexed files + setStatus READY
When updating the variants collection, there are tree possible scenarios:
The first approach will consist in making a Allowing concurrent merges from different studies, it may happen that a document, supposedly non existing in the collection ( To sort this out, the easiest solution is to perform a This second approach will use only update operations, solving the first and the second scenarios at the same time. |
Allow concurrent merge operations for different studies
Add direct loader for the first file in a chromosome to load directly to the variants collection. see Add direct loader for the first file in a chromosome to load directly to the variants collection #354VariantStorageManager#index(List<URI>)
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