Nirvana | The nimble & robust variant annotator | Genomics library

by Illumina C# Version: v3.18.1 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | Nirvana Summary

Nirvana is a C# library typically used in Artificial Intelligence, Genomics applications. Nirvana has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Nirvana provides clinical-grade annotation of genomic variants (SNVs, MNVs, insertions, deletions, indels, and SVs (including CNVs). It can be run as a stand-alone package or integrated into larger software tools that require variant annotation. The input to Nirvana are VCFs and the output is a structured JSON representation of all annotation and sample information (as extracted from the VCF). Optionally, a subset of the annotated data is available in VCF and/or gVCF files. Nirvana handles multiple alternate alleles and multiple samples with ease. The software is being developed under a rigorous SDLC and testing process to ensure accuracy of the results and enable embedding in other software with regulatory needs. Nirvana uses a continuous integration pipeline where millions of variant annotations are monitored against baseline values on a daily basis. Backronym: NImble and Robust VAriant aNnotAtor.

Support

Quality

Security

License

Reuse

Support

Nirvana has a low active ecosystem.

It has 152 star(s) with 32 fork(s). There are 32 watchers for this library.

It had no major release in the last 12 months.

There are 28 open issues and 69 have been closed. On average issues are closed in 40 days. There are 5 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of Nirvana is v3.18.1

Quality

Nirvana has 0 bugs and 0 code smells.

Security

Nirvana has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

Nirvana code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

Nirvana is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

Nirvana releases are available to install and integrate.

Nirvana saves you 3215 person hours of effort in developing the same functionality from scratch.

It has 2928 lines of code, 0 functions and 619 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of Nirvana

Get all kandi verified functions for this library.

Nirvana Key Features

No Key Features are available at this moment for Nirvana.

Nirvana Examples and Code Snippets

No Code Snippets are available at this moment for Nirvana.

Community Discussions

Trending Discussions on Nirvana

ElasticSearch can't get multiple suggestor values from the same document

SWC with JavaScript: How to handle CSS imports and how to absolute imports?

Migrating from Babel to SWC with React

How to do in python , so that a previously printed item from a list, is no longer repeated the next time it is printed

Running a program iteratively on subfolders using the find function in bash

How to add new features to the provider & consumer code without breaking the Pact contract?

return a table with a column with yes or no

Combine arrays in map function

my tailwind utility class does not work in production

Appending data to pickle in python

QUESTION

ElasticSearch can't get multiple suggestor values from the same document

Asked 2022-Mar-11 at 11:54

Can you help me please i have a problem with Completion Suggester in ElasticSearch Example : i have this mapping :

...

ANSWER

Answered 2022-Mar-11 at 11:54

This is the default behavior of current implementations. You can check #31738. Below is one of the comment for an explanation why it is returning only one document/suggestion.

The completion suggester is document-based by design so we cannot return one entry per matching suggestion. It is documented that it returns documents not suggestions and a single input can be indexed in multiple suggestions (if you have synonyms in your analyzer for instance) so it is not trivial to differentiate a match from its variations. Also the completion suggester does not visit all suggestions to select the top N, it has a special structure (a weighted FST) that can visit suggestions in the order of their scores and early terminates the query once enough documents have been found.

Source https://stackoverflow.com/questions/71430872

QUESTION

SWC with JavaScript: How to handle CSS imports and how to absolute imports?

Asked 2022-Feb-21 at 21:57

TL;DR

How can you tell SWC to compile CSS files imported in React components?
How can you tell SWC to compile absolute imports in tests and in React components?

Here is a minimal reproducible example.

Context

We're migrating from Babel to SWC. (I asked a question a little while ago. I'm improving on that question's answer.)

We're migrated the command from:

...

ANSWER

Answered 2022-Jan-31 at 22:53

How can we help SWC understand CSS (or mock CSS modules)? - SWC doesn't understand css natively, and neither did Babel. As you noted, when you were using Babel, the plugin styled-components took care of this. You'll need to do the same with SWC. I can't find an existing SWC plugin that does this, but you can roll your own. Obviously this is a pain, but such is the cost of using new tooling.
How can we help SWC understand absolute imports? - The .swrc options for baseUrl and paths should do what you want, but that, too, seems to have some issues.

You may have better luck creating issues directly in the @swc-node GitHub repo, but given the comments there it feels like you might be SOL for a while. Might be faster/easier to rewrite your tests using one of the libraries that Next supports out of the box.

Source https://stackoverflow.com/questions/70899604

QUESTION

Migrating from Babel to SWC with React

Asked 2022-Jan-09 at 16:03

TL;DR

How to translate a node script like this:

...

ANSWER

Answered 2021-Nov-15 at 22:49

I'll assume your question is only about jest and not about the webpack setup for swc.

I've never used swc myself in jest so this is just a shot in the dark, but I found a package for jest called @sec-node/jest which allows you to use a transformer like:

Source https://stackoverflow.com/questions/69956543

QUESTION

How to do in python , so that a previously printed item from a list, is no longer repeated the next time it is printed

Asked 2021-Nov-16 at 13:22

I recently started learning to program in python, and just for fun I wrote this program, but I need some help.

It's possible that I've complicated things and it can be simplified somehow, but I'm just a beginner.

I have the following code:

...

ANSWER

Answered 2021-Nov-16 at 10:04

Make your random list as a set.

Then for every song you extract from it, pop it from the set

Source https://stackoverflow.com/questions/69986557

QUESTION

Running a program iteratively on subfolders using the find function in bash

Asked 2021-Oct-27 at 09:06

I am trying to run a specific program by looping it through a bunch of subdirectories using the find function, yet nothing seems to happen. Here is my code:

...

ANSWER

Answered 2021-Oct-27 at 09:06

The -maxdepth 1 is telling find to search only in ~/test, not its subdirectories.

find's idea of depth can be a little confusing: since you gave it ~/test as the starting point for the search, it considers that to be at depth 0, items directly inside it to be at depth 1, and items inside those (i.e. in subdirectories of ~/test) to be at depth 2. So if you want it to find things in subdirectories, use -maxdepth 2.

(Just to make things more confusing: if you use something like find ~/test/* ..., then the shell expands the ~/test/* part into a list of files & directories in ~/test and passes those as arguments to find. Therefore, since each of those was given to find as a separate starting point, each of those would be considered depth 0 in its own separate search. In this case, things in the subdirectories would be at depth 1.)

Actually, since you want to search at just a single level, I'd just use a shell wildcard expression:

Source https://stackoverflow.com/questions/69731294

QUESTION

How to add new features to the provider & consumer code without breaking the Pact contract?

Asked 2021-Aug-06 at 00:01

Pipelines

I am trying to get my pipelines as close to pact nirvana as possible, minus the deploying to testing as I am still playing around with the technology.

Note, I am using the open source version of the broker and not pactflow.

Provider Pipeline

build
test
verify against the latest production tagged consumer pact (latest provider is versioned as the git sha, tagged as the git branch)
use can-i-deploy to check the pact matrix if the latest latest tagged production consumer mocks has passed verification against the latest provider version.
deploy
tag the recently deployed version of the provider as production in the pact broker

Consumer Pipeline

build
test and publish to the broker (latest consumer is versioned as the git sha, tagged as the git branch)
webhook executes the verification for the newly published consumer version in the provider pipeline against production tagged provider
use can-i-deploy to check the pact matrix in the broker to determine whether the latest consumer mocks has passed verification against the latest tagged production provider
deploy
tag the recently deployed version of the consumer as production in the pact broker

Problem

This falls apart when I am trying to build a new feature.

Lets say I create a change that breaks the contract between the consumer and provider by changing the providers response to something very different (imagine its a new feature for a consumer). This obviously fails at the verification step within the pipeline as we are checking it against production tagged consumer.

We then alter the consumer mocks (and code) to consume this new response. Then we push to the repo which initiates the CI and fails at the verification step as we are testing against a production tagged provider (not the newest tag with the feature branch name).

We obviously always want to be verifying against a production tagged counterpart (same with can-i-deploy) in case I create a breaking change by accident in either the consumer or provider codebase.

So we have a catch-22 situation; how do we add a new feature that both consumer and provider code will need to be modified for without breaking the recommended pipeline?

...

ANSWER

Answered 2021-Aug-06 at 00:01

https://docs.pact.io/faq#how-can-i-make-a-breaking-change-to-a-provider

If you need to make a breaking change to a provider, you can do it in a multiple step process using the expand and contract pattern.

Add the new fields/endpoints to the provider and deploy. Update the consumers to use the new fields/endpoints, then deploy. Remove the old fields/endpoints from the provider and deploy. At each step of the process, all the contract tests remain green. This pattern is supported well by consumer driven contracts because it is easy for a provider to determine if/when all the consumers have dropped use of the old field by removing it in a local development environment and running the pact verification tests.

Source https://stackoverflow.com/questions/68653621

QUESTION

return a table with a column with yes or no

Asked 2021-Apr-14 at 20:05

I have the following two tables:

Singers

...

ANSWER

Answered 2021-Apr-14 at 19:19

You can ascertain this a number of ways, one way would be using exists

Source https://stackoverflow.com/questions/67097778

QUESTION

Combine arrays in map function

Asked 2021-Mar-09 at 18:37

I have an issue, or at least I'm not having the solution.

I'm getting some API calls via a map and I can console.log all results which is great, but the problem is that I want to combine all the results in one array.

...

ANSWER

Answered 2021-Mar-08 at 22:28

Have you tried pushing them into an array?

Source https://stackoverflow.com/questions/66538047

QUESTION

my tailwind utility class does not work in production

Asked 2021-Feb-28 at 23:02

I found "Nirvana" (or should I say Tailwind) - it's just about how great I find this library/framework! It goes well with Rails - and Webpacker too. In fact, all is well except for this one bugger;

I've got this sneaky little contraption of mine affording quite readable view templates (and yeah - I know - it's obviously flawed in a million ways but it gets the job done, what can I say)

...

ANSWER

Answered 2021-Feb-28 at 23:02

Sometimes the answer is right under your nose - as was the case at hand! I knew it had to do with something happening before I would start 'uploading' to the server and I had my eyes fixed on PostCSS; it certainly paid off!

My tailwind.config.js tells PostCSS what files to vacuum - and it looked like this:

Source https://stackoverflow.com/questions/66413687

QUESTION

Appending data to pickle in python

Asked 2021-Jan-11 at 02:39

I am creating a program which generates a random list of songs, and has a function such that if a user wants to save a song from the random generated list, the user should click the button next to it. Then the user can print the songs he/she saved on a new window, and then I add a function using pickle so that if the user closes and reruns the program the previously saved items are retained and can be reprinted. But an error, how can I implement this correctly

This is the code:

...

ANSWER

Answered 2021-Jan-11 at 02:39

import pickle

lst = [1,2,3]

with open("test.dat", "wb") as msg:
    pickle.dump(lst, msg)

with open("test.dat", "ab+") as msg:
    pickle.dump(lst, msg)

with open("test.dat", "rb") as msg:
    print (pickle.load(msg))

Source https://stackoverflow.com/questions/65660651

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

Vulnerabilities

No vulnerabilities reported

Install Nirvana

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

Find more information at: