mosdepth
Unchained
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mosdepth
- Calculating Average Coverage or Read Depth for a Sequence (WES)
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Why is bedtools genomecov giving me a blank output file?
I'm not sure why that happens, but an alternative to bedtools genomecov is mosdepth. Maybe you can try that tool instead as it's very reliable.
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Is there a tool that quantifies “spatial coverage”, that is what percentage of a reference assembly has a read mapped to it?
I would give mosdepth a look. It can provide depth across a chromosome/contig at each base, or a mean depth for a given window size (eg 1kb), or regions provided within a bed file, or a simple summary of the mean depth across each chromosome/contig.
Unchained
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GNU Units
Anything with a finite (200 is small even) number of units misses the algebraic structure of the problem mentioned in https://news.ycombinator.com/item?id=36988497 wherein multiplying|dividing two things gives you a (potentially) new unit which implies an open ended "space" of units.
To be concrete (hah!), in C++ a template meta-type with 12 signed integer parameters (6 numerators & 6 denominators for rational exponents of SI base units) might be one way to model it.
Unlike C++ template stuff, Nim macros (like Lisp macros) makes metaprogramming more like procedural programming - just against abstract syntax trees. I think that helps to shield some of this type complexity from users, but the documentation README https://github.com/SciNim/Unchained does better job than I can in an HN comment.
Of course, for unit system conversion, the number of dimensions (6 in SI, 3 in CGS/Gaussian) changes. So, for full generality you need compile-time (if you want static type integration/CT errors) linear algebra over a rational field (at least & conventionally) to project|inverse project. That might be theoretically possible in C++. I would think it very un-fun and unlikely to ever have been done. There's probably a Mathematica package, though.
- Please Put Units in Names
- Pint: Makes Units Easy -Python
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Atlas, a (hopefully) better engineering IDE
I've recently written a units library for Nim [0]. It's still WIP, but it's already proven extremely useful for me as a physicist.
Thanks to Nim's strong type system and metaprogramming features, it allows for a fully compile time design, without any runtime overhead (in form of special unit objects or such things; everything is a `distinct float`).
In addition Nim's unicode support, the code even looks nice!
A more complex use case (I can link more if desired): [1]
[0]: https://github.com/SciNim/Unchained/
[1]: https://github.com/SciNim/Unchained/tree/master/examples
What are some alternatives?
nimbus-eth1 - Nimbus: an Ethereum Execution Client for Resource-Restricted Devices
SI - A header only C++ library that provides type safety and user defined literals for physical units
nim-plotly - plotly wrapper for nim-lang
moe - A command line based editor inspired by Vim. Written in Nim.
nimview - A Nim/Webview based helper to create Desktop/Server applications with Nim/C/C++ and HTML/CSS
INim - Interactive Nim Shell / REPL / Playground
zen
adventofcode2022 - Advent of Code 2022 solutions in Nim
phpmnd - PHP Magic Number Detector
Neel - A Nim library for making Electron-like HTML/JS GUI apps, with full access to Nim capabilities.
kal - A powerful, easy-to-use, and easy-to-read programming language for the future.