BedUtils | Java classes and abstractions to assist with processing bed | Learning library

by njdbickhart Java Version: Current License: No License

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

kandi X-RAY | BedUtils Summary

BedUtils is a Java library typically used in Tutorial, Learning applications. BedUtils has no bugs, it has no vulnerabilities and it has low support. However BedUtils build file is not available. You can download it from GitHub.

A collection of Java classes and abstractions to assist with processing bed files. Translates several algorithms from Aaron Quinlan's Bedtools to Java

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Quality

Security

License

Reuse

Support

BedUtils has a low active ecosystem.

It has 5 star(s) with 0 fork(s). There are 3 watchers for this library.

It had no major release in the last 6 months.

BedUtils has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of BedUtils is current.

Quality

BedUtils has no bugs reported.

Security

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

License

BedUtils does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

BedUtils releases are not available. You will need to build from source code and install.

BedUtils has no build file. You will be need to create the build yourself to build the component from source.

Top functions reviewed by kandi - BETA

kandi has reviewed BedUtils and discovered the below as its top functions. This is intended to give you an instant insight into BedUtils implemented functionality, and help decide if they suit your requirements.

Initialize the components
Intersects the specified file and returns the intersectedbed map
Add intersection to the intersect
Run the intersection
Intersect two membedbed maps
Get a merge set
Calculates the intersection of the two BedMap objects
Get a merge set
Loads the data from the specified file
Loads the contents of the file in the file
Combine the specified BID with the specified map
Sorts the chars in ascending order
Checks the overlap between two intervals
Sets the number of values from the file
Sets the information from the specified line
Convert a comma - separated string to an integer array
Return a copy of the merged map
Determines if a new BedEntry overlaps with an existing BID
Sets the look and feel
Get sort order
Writes the merge fragments
Runs the merge
Checks to see if the specified Chars overlap the specified character
Inserts a bin entry for the specified bin
Convert UCSC to array of strings
Retrieve the closest matches from a file
Retrieve the closest Cluster from the specified file

Get all kandi verified functions for this library.

BedUtils Key Features

No Key Features are available at this moment for BedUtils.

BedUtils Examples and Code Snippets

No Code Snippets are available at this moment for BedUtils.

Community Discussions

Trending Discussions on Learning

How do purely functional languages handle index-based algorithms?

How can I fix this : Warning: the fonts "Times" and "Times" are not available for the Java logical font "Serif"

Keras AttributeError: 'Sequential' object has no attribute 'predict_classes'

How do I fix CLIENT_MISSING_INTENTS error?

Getting error 'digital envelope routines', reason: 'unsupported', code: 'ERR_OSSL_EVP_UNSUPPORTED'

Vue 3 passing array warning: Extraneous non-props attributes were passed to component but could not be automatically inherited

TypeError: match.loader.options.plugins is not a function

Group and create three new columns by condition [Low, Hit, High]

What should the result be when assigning a variable to a reference to itself, in-between modified and then returned by a function call?

Flutter (2.5) - A splash screen was provided to Flutter, but this is deprecated

QUESTION

How do purely functional languages handle index-based algorithms?

Asked 2022-Apr-05 at 12:51

I have been trying to learn about functional programming, but I still struggle with thinking like a functional programmer. One such hangup is how one would implement index-heavy operations which rely strongly on loops/order-of-execution.

For example, consider the following Java code:

...

ANSWER

Answered 2022-Mar-07 at 21:17

This is not an index-heavy operation, in fact you can do this with a one-liner with scanl1 :: (a -> a -> a) -> [a] -> [a]:

Source https://stackoverflow.com/questions/71387267

QUESTION

How can I fix this : Warning: the fonts "Times" and "Times" are not available for the Java logical font "Serif"

Asked 2022-Mar-27 at 13:54

system：Mac OS software：AnyLogic 8 Personal Learning Edition 8.7.6 language: Java

When I run my model, the console print this info:

Warning: the fonts "Times" and "Times" are not available for the Java logical font "Serif", which may have unexpected appearance or behavior. Re-enable the "Times" font to remove this warning.

...

ANSWER

Answered 2021-Aug-01 at 11:11

We also recently had this issue on a mac running the latest public beta of Monterey.

For some reason the Times font was no longer installed or active on the Mac.

You can check in FontBook

You can simply reinstall it

I struggled to find a source online - her is one suggestion - https://www.freebestfonts.com/timr45w-font

Source https://stackoverflow.com/questions/68608157

QUESTION

Keras AttributeError: 'Sequential' object has no attribute 'predict_classes'

Asked 2022-Mar-23 at 04:30

Im attempting to find model performance metrics (F1 score, accuracy, recall) following this guide https://machinelearningmastery.com/how-to-calculate-precision-recall-f1-and-more-for-deep-learning-models/

This exact code was working a few months ago but now returning all sorts of errors, very confusing since i havent changed one character of this code. Maybe a package update has changed things?

I fit the sequential model with model.fit, then used model.evaluate to find test accuracy. Now i am attempting to use model.predict_classes to make class predictions (model is a multi-class classifier). Code shown below:

...

ANSWER

Answered 2021-Aug-19 at 03:49

This function were removed in TensorFlow version 2.6. According to the keras in rstudio reference

update to

Source https://stackoverflow.com/questions/68836551

QUESTION

How do I fix CLIENT_MISSING_INTENTS error?

Asked 2022-Mar-11 at 10:51

I started learning about discord.js but now I am facing this issue. I tried some googling but couldn't manage to fix it.

...

ANSWER

Answered 2021-Aug-07 at 16:34

You need to specify the events which you want your bot to receive using gateway intents.

Instead of

const client = new Discord.Client();

Use

const client = new Discord.Client({ intents: [Enter intents here] })

For example

const client = new Discord.Client({ intents: ["GUILDS", "GUILD_MESSAGES"] })

Here's another useful link: https://discord.com/developers/docs/topics/gateway

Source https://stackoverflow.com/questions/68694195

QUESTION

Getting error 'digital envelope routines', reason: 'unsupported', code: 'ERR_OSSL_EVP_UNSUPPORTED'

Asked 2022-Mar-05 at 09:54

I got this error when learning Next.js, using npx create-next-app command according to site documentation here https://nextjs.org/docs/api-reference/create-next-app. Everything works until I start the server,

Error stack:

...

ANSWER

Answered 2021-Nov-24 at 21:38

I found this solution https://github.com/webpack/webpack/issues/14532

if using bash just run NODE_OPTIONS=--openssl-legacy-provider before any command
adding NODE_OPTIONS=--openssl-legacy-provider to package.json

Source https://stackoverflow.com/questions/69719601

QUESTION

Vue 3 passing array warning: Extraneous non-props attributes were passed to component but could not be automatically inherited

Asked 2022-Feb-26 at 21:48

please, I'm learning a VueJS 3 and I have probably begineer problem. I have warn in browser developer console like this one:

The Message is:

...

ANSWER

Answered 2021-Aug-16 at 13:32

The ItemProperties component has multiple root nodes because it renders a list in the root with v-for.

Based on the class name (infobox-item-properties), I think you want the class to be applied to a container element, so a simple solution is to just add that element (e.g., a div) in your component at the root:

Source https://stackoverflow.com/questions/68803137

QUESTION

TypeError: match.loader.options.plugins is not a function

Asked 2022-Feb-24 at 05:03

I am trying to use tailwindCSS in a ReactJS app

These are the scripts commands in package.json file

...

ANSWER

Answered 2021-Dec-18 at 22:00

It looks like the Tailwind configuration from CRACO is not needed anymore.

https://github.com/facebook/create-react-app/issues/11771#issuecomment-997217680

Look at Tailwind 3.0 install steps: https://tailwindcss.com/docs/guides/create-react-app

Source https://stackoverflow.com/questions/70403417

QUESTION

Group and create three new columns by condition [Low, Hit, High]

Asked 2022-Feb-10 at 16:22

I have a large dataset (~5 Mio rows) with results from a Machine Learning training. Now I want to check to see if the results hit the "target range" or not. Lets say this range contains all values between -0.25 and +0.25. If it's inside this range, it's a Hit, if it's below Low and on the other side High.

I now would create this three columns Hit, Low, High and calculate for each row which condition applies and put a 1 into this col, the other two would become 0. After that I would group the values and sum them up. But I suspect there must be a better and faster way, such as calculate it directly while grouping. I'm happy for any idea.

Data ...

ANSWER

Answered 2022-Feb-10 at 16:13

You could use cut to define the groups and pivot_table to reshape:

Source https://stackoverflow.com/questions/71068392

QUESTION

What should the result be when assigning a variable to a reference to itself, in-between modified and then returned by a function call?

Asked 2022-Feb-02 at 00:42

#include 

int& addOne(int& x)
{
    x += 1;
    return x;
}

int main()
{
    int x {5};
    addOne(x) = x;
    std::cout << x << ' ' << addOne(x);
}

...

ANSWER

Answered 2022-Feb-02 at 00:42

Since C++17 the order of evaluation is specified such that the operands of = are evaluated right-to-left and those of << are evaluated left-to-right, matching the associativity of these operators. (But this doesn't apply to all operators, e.g. + and other arithmetic operators.)

So in

Source https://stackoverflow.com/questions/70909321

QUESTION

Flutter (2.5) - A splash screen was provided to Flutter, but this is deprecated

Asked 2022-Jan-19 at 05:24

I am new to flutter and recently tried to develop a test app for learning sake with latest version Flutter 2.5. By looking at some tutorial online, I have added flutter_native_splash: ^1.2.3 package for splash screen. And works fine.

However, when I launch app for the first time, it shows following debug message

W/FlutterActivityAndFragmentDelegate(18569): A splash screen was provided to Flutter, but this is deprecated. See flutter.dev/go/android-splash-migration for migration steps.

After visiting the above link, I am not able to understand much what is supposed to be done.

Code in pubspec.yaml

...

ANSWER

Answered 2022-Jan-19 at 05:24

To avoid that warning you just need to remove that API usage from your project. Remove these lines of code from the AndroidManifest.xml file.

Previously, Android Flutter apps would either set io.flutter.embedding.android.SplashScreenDrawable in their application manifest, or implement provideSplashScreen within their Flutter Activity. This would be shown momentarily in between the time after the Android launch screen is shown and when Flutter has drawn the first frame. This is no longer needed and is deprecated – Flutter now automatically keeps the Android launch screen displayed until Flutter has drawn the first frame. Developers should instead remove the usage of these APIs. - source

UPDATE (FLUTTER 2.8.0)

As per the flutter 2.8.0 update, The newly created project doesn't have this warning.

They removed unused API from Androidmanifest.yml but still have belove mentioned code.

Source https://stackoverflow.com/questions/69232006

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

Vulnerabilities

No vulnerabilities reported

Install BedUtils

You can download it from GitHub.
You can use BedUtils like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the BedUtils component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

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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