Nirvana | The nimble & robust variant annotator | Genomics library

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

kandi X-RAY | Nirvana Summary

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.
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            kandi-support Support

              Nirvana has a low active ecosystem.
              It has 152 star(s) with 32 fork(s). There are 32 watchers for this library.
              OutlinedDot
              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

            kandi-Quality Quality

              Nirvana has 0 bugs and 0 code smells.

            kandi-Security 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.

            kandi-License 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.

            kandi-Reuse 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.

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            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

            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
            1. 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.
            2. 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 .
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            https://github.com/Illumina/Nirvana.git

          • CLI

            gh repo clone Illumina/Nirvana

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            git@github.com:Illumina/Nirvana.git

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