octopus | Bayesian haplotype-based mutation | Genomics library

 by   luntergroup C++ Version: v0.7.4 License: MIT

kandi X-RAY | octopus Summary

kandi X-RAY | octopus Summary

octopus is a C++ library typically used in Artificial Intelligence, Genomics applications. octopus has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time.
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            kandi-support Support

              octopus has a low active ecosystem.
              It has 280 star(s) with 34 fork(s). There are 17 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 30 open issues and 213 have been closed. On average issues are closed in 52 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of octopus is v0.7.4

            kandi-Quality Quality

              octopus has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              octopus is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              octopus releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            octopus Key Features

            No Key Features are available at this moment for octopus.

            octopus Examples and Code Snippets

            No Code Snippets are available at this moment for octopus.

            Community Discussions

            QUESTION

            How to disalbe Ceph Dashboard Anonymous Access?
            Asked 2021-Jun-10 at 10:32

            I have installed a Ceph cluster V15 (Octopus). Following the general setup guide a Grafana Dashboard is installed during bootstrapping the cluster. This is a nice feature. But the dashboard can be access on port :3000 from anonymous without authentication.

            I guess this is because of the configuration of the anonymous mode in /etc/grafana/grafana.ini:

            ...

            ANSWER

            Answered 2021-Jun-10 at 10:32

            There's an instance of the grafana.ini file on the grafana host:

            Source https://stackoverflow.com/questions/67909874

            QUESTION

            "INVALID_PARAMETERS" error response when sending a PUT request to Email Octopus
            Asked 2021-Jun-08 at 04:53

            When a user signs up,
            we send an HTTPS PUT request to Email Octopus
            in order to add that user to an email marketing list.

            This PUT request includes the following user`s data:

            • email
            • first name
            • last name
            • country

            We followed the guidelines here:
            https://emailoctopus.com/api-documentation

            We also followed the same syntax as mentioned here:
            https://emailoctopus.com/api-documentation/lists/create-contact

            However, we get an "Invalid Parameters" response.

            Any idea what are we doing wrong?

            We send the following request:

            ...

            ANSWER

            Answered 2021-Jun-08 at 04:53

            After discussing with EmailOctopus support,
            we fixed the issue by doing the following:
            We added the following header to our HTTPS request:

            Source https://stackoverflow.com/questions/67873887

            QUESTION

            Octopus Deploy with Terraform module from Git
            Asked 2021-May-27 at 22:20

            I'm not exactly sure where my issue is here, but I believe it is on the octopus side. I am trying to deploy my octopus worker. There are essentially 4 steps to my deploy script.

            1. Update kube-config
              • aws eks update-kubeconfig
            2. Run helm upgrade
              • helm upgrade --install
            3. Create IAM Policy via terraform
              • cd terraform
              • terraform init
                • *With s3 backend parameters set
              • terraform plan -var-file=default.tfvars -out=tfplan
              • terraform apply tfplan
            4. Create IAM serviceaccount attach IAM policy to octopus worker role
              • eksctl create iamserviceaccount --attatch-policy-arn={iam-policy-arn}

            I've left out some steps/flags, but this is the gist of it. I have a public github repo that houses all of my terraform modules. Inside this repo, I have a terraform directory where I reference that public repo:

            ...

            ANSWER

            Answered 2021-May-27 at 22:20

            Ended up finding my answer. The octopus worker must have got some sort of interactive prompt because I was trying to source the git repo through ssh. Changed it to HTTPS and worked fine.

            Source https://stackoverflow.com/questions/67711639

            QUESTION

            Azure DevOps - Package Application for Octopus: System.IO.IOException: The parameter is incorrect *
            Asked 2021-May-18 at 06:28

            I'm trying to package my application into a zip file, in order to send it to Octopus.

            The log looks like this:

            ...

            ANSWER

            Answered 2021-May-18 at 06:28

            I think the real issue is that you did not set the right Sources Path for the project under the hosted agent.

            If your repos's branch has the folder called _KFPortal-CI, then you should set the Sources Path to

            Source https://stackoverflow.com/questions/67577234

            QUESTION

            Why is my helper method not activating recursively?
            Asked 2021-May-13 at 03:52

            I have a Binary Search Tree and I am trying to trace recursively in order through the tree and append each key,value to a list. It is only appending the first key,value to the list and not going through the list in order. I pasted my code below, along with the test code I used at the bottom. Any help on how to get past this issue is super appreciated!

            ...

            ANSWER

            Answered 2021-May-13 at 03:52

            QUESTION

            Generating random results without repetition
            Asked 2021-May-03 at 00:55

            I've been trying different ways to randomize the questions in a little quiz I'm making, but all the methods I'm finding are using a function that will still repeat items when you end the function and call it again. I've tried using pop to do it but have only run into that same issue.

            Here is some of my code for reference.

            ...

            ANSWER

            Answered 2021-May-03 at 00:55

            You didn't show how you try to get random elements so you could do something what changes order back to original.

            You can use random.shuffle(list) to set random order on the list.
            And then you can use for item on list: ... to get items without repetition.

            Source https://stackoverflow.com/questions/67359593

            QUESTION

            How to perform a variable substitution for an appsettings.json file in AWS CodeDeploy?
            Asked 2021-Apr-27 at 23:25

            I spent some time recently seeing if I could get my Azure Devops .NET Core-based pipelines "translated" to AWS CodeDeploy (our web infrastructure is in AWS), but for the life of me I cannot figure out how to update the appsettings.json files with any environment-specific values.

            Azure Devops, Bamboo, Octopus, I think even Jenkins and TeamCity support variable substitution on JSON configuration files, but I just cannot figure out how to make that happen in AWS CodeDeploy.

            Is there a way to do this? Is there some common workaround that people are using?

            ...

            ANSWER

            Answered 2021-Apr-27 at 23:25

            I ended up in a fairly lengthy discussion with AWS support (though I was trying to make a feature request) and what came out of it was... AWS CodeDeploy just doesn't support that.

            Now, IMO, this really demonstrates a lack of maturity in the product, and/ or an unwillingness to support traditional .NET Core code bases, but naturally it can't be left like that. So... I built a tool.

            Github now has an open-source project at https://github.com/jholovacs/varsub that allows you to perform a variable substitution on a JSON file using a secure parameter, specifying the path to the property value.

            I hope this saves someone else some headaches.

            Source https://stackoverflow.com/questions/67102464

            QUESTION

            how can I make the arrow border right background colorful
            Asked 2021-Apr-06 at 20:40

            I need to make the arrow of the right side colorful #2b6a83

            ...

            ANSWER

            Answered 2021-Apr-06 at 20:40

            You where almost there ;) Just add the background-color: #2b6a83 to your :before and :after elements. Be aware that an :after element with a position absolute will be rendered in front of the parent element. You can fix that by using a simple negative z-index like z-index: -1:

            Source https://stackoverflow.com/questions/66976004

            QUESTION

            Questions in android app gets repeated when shuffling them
            Asked 2021-Mar-29 at 11:41

            I am new to the whole coding world. And I am currently creating a learning app for kids, and one of the categories included is taking a quiz. I wanted to shuffle all the questions and I was able to do so but the problem I am facing now is that the questions gets repeated

            here is the code i used for Quiz questions activity

            ...

            ANSWER

            Answered 2021-Mar-29 at 11:41

            The issue is you're calling the shuffle function in updateQuestion. So it updates the questionArray everytime updateQuestion method is called.

            Solution

            Remove shuffleQuestions(); from updateQuestion method and add it before updateQuestion(); in onCreate method such that shuffling happens once in the beginning when the class is loaded.

            Updated source code

            Source https://stackoverflow.com/questions/66853401

            QUESTION

            FFmpeg Drawbox Errors?
            Asked 2021-Mar-12 at 01:08

            Using ffmpeg version 4.3.2.

            Command:

            ...

            ANSWER

            Answered 2021-Mar-12 at 01:08

            You're using arbitrary, unsupported variables. Refer to the drawbox documentation for a list of supported variables (under the section "The parameters for x, y, w and h and t are expressions containing the following constants").

            I can only guess what you are trying to do, but here is a simplified valid example:

            Source https://stackoverflow.com/questions/66576749

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

            Vulnerabilities

            No vulnerabilities reported

            Install octopus

            You can download it from GitHub.

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