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https://github.com/brentp/variantkey-nim

nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64

https://github.com/brentp/variantkey-nim

Science Score: 13.0%

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Keywords

genomics variant
Last synced: 5 months ago · JSON representation

Repository

nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64

Basic Info
  • Host: GitHub
  • Owner: brentp
  • License: mit
  • Language: C
  • Default Branch: master
  • Homepage:
  • Size: 21.5 KB
Statistics
  • Stars: 4
  • Watchers: 2
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Topics
genomics variant
Created about 7 years ago · Last pushed about 7 years ago
Metadata Files
Readme License

README.md

variantkey

nim wrapper for variantkey.

This wrapper can encode+decode about 5 million variants per second. The entirety of the API exposed by this library is demonstrated below:

``` import variantkey

var chrom = "19" pos = 3323934'u32 # encode e = encode(chrom, pos, "A", "T")

assert e.exact echo e # 10959892387821256704 echo e.decode # (chrom: "19", position: 3323934, reference: "A", alternate: "T", exact: true)

longer variants are encoded with a hash

e = encode("1", 878111, "CAGGGGCCCCCGGGCTCCGGACCCCCCACCCCGTCCCGGGACTCTGCCCGGCGAGCCCCCCGGAA", "C")

the reference and alternate are not set upon decoding.

echo e # (chrom: "1", position: 878111, reference: "", alternate: "") ```

Owner

  • Name: Brent Pedersen
  • Login: brentp
  • Kind: user
  • Location: Oregon, USA

Doing genomics

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Last synced: 11 months ago

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Brent Pedersen b****e@g****m 7

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  • nicolaasuni (1)
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