https://github.com/brentp/d4-nim
nim-lang wrapper for https://github.com/38/d4-format
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 2 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (3.8%) to scientific vocabulary
Keywords
Repository
nim-lang wrapper for https://github.com/38/d4-format
Basic Info
- Host: GitHub
- Owner: brentp
- License: mit
- Language: Nim
- Default Branch: master
- Size: 26.4 KB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
d4-nim
This is a nim wrapper for Hao Hou's d4 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. 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", 249200100): echo iv # (tuple of start:uint32, end:uint32, value:int32)
var start = 249200100'u32 var stop = 249240621'u32
each entry in vals contains the depth for pos-start
var vals:seq[int32] = d4f.values("1", start, stop) ```
Owner
- Name: Brent Pedersen
- Login: brentp
- Kind: user
- Location: Oregon, USA
- Twitter: brent_p
- Repositories: 220
- Profile: https://github.com/brentp
Doing genomics
GitHub Events
Total
- Watch event: 1
- Issue comment event: 1
- Push event: 1
- Pull request review event: 3
- Pull request review comment event: 3
- Pull request event: 2
- Fork event: 1
- Create event: 1
Last Year
- Watch event: 1
- Issue comment event: 1
- Push event: 1
- Pull request review event: 3
- Pull request review comment event: 3
- Pull request event: 2
- Fork event: 1
- Create event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Brent Pedersen | b****e@g****m | 22 |
| Cade Mirchandani | c****n@u****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 10 hours
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 10 hours
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- cademirch (1)
Pull Request Authors
- cademirch (1)