https://github.com/brentp/d4-nim

nim-lang wrapper for https://github.com/38/d4-format
https://github.com/brentp/d4-nim

bioinformatics genomics high-throughput-sequencing

Last synced: 25 days ago
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nim-lang wrapper for https://github.com/38/d4-format

• Host: GitHub
• URL: https://github.com/brentp/d4-nim
• Owner: brentp
• License: mit
• Created: 2020-05-15T18:34:58.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2024-08-27T19:22:24.000Z (2 months ago)
• Last Synced: 2024-09-20T00:04:12.698Z (about 2 months ago)
• Topics: bioinformatics, genomics, high-throughput-sequencing
• Language: Nim
• Size: 22.5 KB
• Stars: 4
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# d4-nim

This is a [nim](https://nim-lang.org) wrapper for Hao Hou's [d4](https://github.com/38/d4-format) which

can be thought of as a way to store integer data in a compressed array. A common use-case will be depth storage

and querying. His library also has a command-line depth extractor that is faster than [mosdepth](https://github.com/brentp/mosdepth).

The extracted (compressed) file can quickly queried for summary info such as mean depth of a region.

Usage in nim looks like:

```Nim

var d4f:D4

doAssert d4f.open("hg002.d4")

echo d4f.chromosomes # ordered table

echo d4f.chromosomes["1"]

for iv in d4f.query("1", 249_200_100):

  echo iv # (tuple of start:uint32, end:uint32, value:int32)

var start = 249_200_100'u32

var stop = 249_240_621'u32

# each entry in vals contains the depth for pos-start

var vals:seq[int32] = d4f.values("1", start, stop)

```