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4dn-dcic / pairix

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
MIT License
83 stars 13 forks source link

assume symmetrical query #41

Closed blajoie closed 6 years ago

blajoie commented 6 years ago

First - love the tool, worked right out of the box. 2D queries on BEDPE will be quite powerful, looking forward to formal tabix support!

One suggestion, if one queries via only a single coordinate, can the tool assume a symmetrical query? e.g. change query internally pairix -h test.bedpe.gz '1:1387294-1468095' to pairix -h test.bedpe.gz '1:1387294-1468095|1:1387294-1468095'

The command, "pairix -h test.bedpe.gz '1:1387294-1468095'" currently returns nothing, I would suspect most users would intend for the tool to run the query, "pairix -h test.bedpe.gz '1:1387294-1468095|1:1387294-1468095'", given the original input.

Thoughts?

SooLee commented 6 years ago

Hi blajoie,

Thank you for your feedback! That's a very good point. Will be in in the next version. :)

Best, Soo