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Check for a strand column in the tabix-indexed file

Open kathyxchen opened this issue 7 years ago • 0 comments

If there is strand information for the genomic features dataset, we should be able to handle this.

We may add a parameter about strandedness (this relates to the "wrapper non strand specific module" that I refer to in PR #25, so we might be able to just pass that information along to the sampler/model controller). In the documentation, we should include our assumption about which column the strand information is in. Another option is we could allow the user to specify which column is the strand column in their dataset.

Side note: In the future, we may even incorporate score information associated with a feature's genomic coordinates. If we get up to that level of complexity, we might enforce the column ordering of [chrom, start, end, feature, strand, score]. If we have only one of strand or score, assume it is the last column. If we have both, it must be in [strand, score] order.

kathyxchen avatar Apr 19 '18 15:04 kathyxchen