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

nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64
https://github.com/brentp/variantkey-nim

genomics variant

Last synced: 16 days ago
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nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64

• Host: GitHub
• URL: https://github.com/brentp/variantkey-nim
• Owner: brentp
• License: mit
• Created: 2018-12-19T00:10:17.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2018-12-19T23:17:06.000Z (about 6 years ago)
• Last Synced: 2024-10-30T13:05:32.063Z (2 months ago)
• Topics: genomics, variant
• Language: C
• Homepage:
• Size: 21.5 KB
• Stars: 4
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# variantkey

nim wrapper for [variantkey](https://github.com/Genomicsplc/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: "")

```