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The pipeline could ingest variants from input/refsnp-chrMT.json and output them in variants.txt
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{ "allele": { "spdi": { "seq_id": "YP_003024031.1", "position": 100, "deleted_sequence": "N", "inserted_sequence": "N" } }, "hgvs": "YP_003024031.1:p.Asn101=" }
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The LinesProcessor judge whether an allele is mutated by check whether the deleted_sequence or inserted_sequence is null.
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Use ItemReader/ItemWriter to do the I/O job, chunkSize should be configured in application.properties
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View Code? Open in Web Editor NEWa pipeline demo to ingest variants from dbSNP