hap.py | Haplotype VCF comparison tools | Genomics library

by Illumina C++ Version: v0.3.15 License: Non-SPDX

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kandi X-RAY | hap.py Summary

hap.py is a C++ library typically used in Artificial Intelligence, Genomics applications. hap.py has no bugs, it has no vulnerabilities and it has low support. However hap.py has a Non-SPDX License. You can download it from GitHub.

This is a set of programs based on [htslib] to benchmark variant calls against gold standard truth datasets. To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. We also have a script to perform comparisons only based on chromosome, position, and allele identity. This comparison will not resolve haplotypes and only verify that the same alleles were observed at the same positions (e.g. for comparison of somatic callsets). More information can be found below in the [usage section] #usage).

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hap.py has a low active ecosystem.

It has 349 star(s) with 115 fork(s). There are 41 watchers for this library.

It had no major release in the last 12 months.

There are 101 open issues and 60 have been closed. On average issues are closed in 31 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of hap.py is v0.3.15

Quality

hap.py has no bugs reported.

Security

hap.py has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

hap.py has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

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hap.py releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

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hap.py Key Features

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hap.py Examples and Code Snippets

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Community Discussions

Trending Discussions on hap.py

Permission denied when calling library function

QUESTION

Permission denied when calling library function

Asked 2021-Mar-25 at 21:18

I am attempting to run a tutorial https://slundberg.github.io/shap/notebooks/Census%20income%20classification%20with%20XGBoost.html

where I'm stuck at

...

ANSWER

Answered 2021-Mar-25 at 21:18

The problem here is that a cache function tried to make a directory in /usr/local/lib/python3.8/dist-packages/shap/ which requires sudo permission.

The solution is to run sudo, I think only once for each dataset.

Or have installed a personal version of shap

Source https://stackoverflow.com/questions/66807617

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install hap.py

You can download it from GitHub.

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