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zaeleus / noodles

Bioinformatics I/O libraries in Rust
MIT License
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Number of variants from index file #195

Closed kriestof closed 1 year ago

kriestof commented 1 year ago

Is it possible to get number of variants from tabix/csi file?

From what I find it should be (here and here).

Sorry for asking question here, but could not find better spot. I just want to indicate some progress information while loading vcf. Of course it's non-critical feature.

zaeleus commented 1 year ago

Sum the mapped record counts of each reference sequence in the index, e.g., noodles-csi/examples/csi_count.rs. This works for any of the binning index formats (BAI, CSI, and tabix).

Sorry for asking question here, but could not find better spot.

No problem! You can use discussions if you have general questions and don't want to open an issue.

kriestof commented 1 year ago

Ok, closing. Thank you for the answer. Should have checked better with examples. Next time I will use discussion.