JAFFA | step pipeline that takes either raw RNA | Genomics library

by Oshlack C++ Version: version-2.3 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(6)Vulnerabilities Install Support

kandi X-RAY | JAFFA Summary

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

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions. It will output the names and locations of candidate gene fusions along with the cDNA sequence of their breakpoints. JAFFA is based on the idea of comparing a transcriptome (e.g. in a cancer sample) against a reference transcriptome. In this way, it is a transcript-centric approach rather than a genome-centric approach like other fusion finders. In validation studies, JAFFA performed well over a range of read lengths - from 50bp to full-length transcripts and on single and paired-end reads. See our wiki for downloads and instructions.

Support

Quality

Security

License

Reuse

Support

JAFFA has a low active ecosystem.

It has 58 star(s) with 19 fork(s). There are 5 watchers for this library.

It had no major release in the last 12 months.

There are 7 open issues and 74 have been closed. On average issues are closed in 280 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of JAFFA is version-2.3

Quality

JAFFA has no bugs reported.

Security

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

License

JAFFA 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.

Reuse

JAFFA releases are available to install and integrate.

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 JAFFA

Get all kandi verified functions for this library.

JAFFA Key Features

No Key Features are available at this moment for JAFFA.

JAFFA Examples and Code Snippets

No Code Snippets are available at this moment for JAFFA.

Community Discussions

Trending Discussions on JAFFA

How can I debug maven dependency problems when mvn dependency-tree doesn't work?

Sending message with Spring Integration to ActiveMQ Artemis topic

Wikipedia API cloud of confusion: `list` vs `generator` vs `search`

Why do I get a CannotAcquireResourceException while trying to connect, when I extend AbstractComboPooledDataSource?

$.getJSON - display individual headers

Why does C3p0's ComboPooledDataSource successfully connect to a database, but its clone doesn't?

QUESTION

How can I debug maven dependency problems when mvn dependency-tree doesn't work?

Asked 2019-Jun-14 at 11:41

I am trying to figure out why IntelliJ is using the wrong version (8.1.1 instead of 8.1.2) of one of my project's Java files. The IntelliJ project is a maven project with many dependencies.

To debug, I tried to use the following from the command line:

...

ANSWER

Answered 2019-Jun-14 at 11:24

First of all, try dependency:tree without verbose. If this does not work out, you can try to add the "dependency convergence" rule (an enforcer rule).

It will fail if you have conflicting versions of the same dependency and this conflict is not resolved in the dependencyManagement. Furthermore, it shows where the conflicting places come from.

Furthermore, if you just want to fix a given version, you can do so in the dependencyManagement.

Source https://stackoverflow.com/questions/56596896

QUESTION

Sending message with Spring Integration to ActiveMQ Artemis topic

Asked 2018-Jun-14 at 14:55

Goal

I would like to send a message to a topic which I will process later with a client applications. For this purpose I use Spring Boot and Spring Integration Java DSL with its JMS module. As a message broker I use a native ActiveMQ Artemis.

Here is my setup

DemoApplication.java

...

ANSWER

Answered 2018-Jun-14 at 13:57

When a message is sent to a topic and auto-creation is enabled for both addresses and queues only the address will be created and not a queue. If a queue were created automatically and the message was put into the queue that would violate the semantics of a topic. A subscription queue on a topic address is only created in response to a subscriber. Therefore, you need a subscriber on the topic before you send the message otherwise the message will be dropped (in accordance with topic semantics).

Source https://stackoverflow.com/questions/50854011

QUESTION

Wikipedia API cloud of confusion: `list` vs `generator` vs `search`

Asked 2018-May-08 at 10:09

My goal is to write an API search of Wikipedia that will:

Return pages only in the category "English language films"
Of those, return pages only beginning with the letters "Avatar" (or anything, really, just using those letters for an example)
Of those, give me the url, the title, the date, a summary, and the main page image.

So far I've tried three things, none of which seem to be able to do exactly what I want.

PROBLEM: list=allpages is just generally useless

Here's a search with list=allpages:

https://en.wikipedia.org/w/api.php?action=query&format=json&prop=info%7Cpageimages%7Cextracts&list=allpages&inprop=url%7Cdisplaytitle&piprop=name%7Cthumbnail%7Coriginal&pithumbsize=100&exintro=1&explaintext=1&apprefix=Avatar&aplimit=3

Here's the result (just the first 3 pages):

...

ANSWER

Answered 2018-May-08 at 10:09

On a high level, list modules generate some list of pages (e.g. the pages most recently edited). Sometimes they include some additional information but mostly they are just meant to give you a list of pages. Prop modules operate on a list of pages and add some kind of extra information to each; the list can be determined by the client (via parameters like titles or pageids) or a list module (used as generator= instead of list=). You can use list= and prop= "together" but all that does is create two separate lists (one of which will be empty and not shown because there is no titles or generator parameter).

Your generator queries are fine; you'll need pilicense=any if you want non-free images in the output. Maybe you found some outdated documentation that does not mention that?

You can use intitle:... in the search term for title search (see docs).

Source https://stackoverflow.com/questions/50161442

QUESTION

Why do I get a CannotAcquireResourceException while trying to connect, when I extend AbstractComboPooledDataSource?

Asked 2017-Oct-21 at 13:52

In a Tomcat 8.5.15 environment using an Oracle 11 database, I want to implement a data source that handles encrypted passwords in the context.xml. For example, instead of having:

...

ANSWER

Answered 2017-Oct-21 at 13:52

The error was a result of a class loading problem, where the Oracle classes were being loaded from multiple jars (%CATALINA_HOME%\lib\ojdbc7-12.1.0.2.0.jar and %CATALINA_HOME%\webapps\my-webapp-1.0.0\WEB-INF\lib\ojdbc7-12.1.0.2.0.jar) by different class loaders. When I deleted %CATALINA_HOME%\webapps\my-webapp-1.0.0\WEB-INF\lib\ojdbc7-12.1.0.2.0.jar, my problem went away.

These sources (1, 2, 3) discuss this in more detail.

Source https://stackoverflow.com/questions/45239142

QUESTION

$.getJSON - display individual headers

Asked 2017-Sep-26 at 01:53

I'm new to JQuery and JSON.

I am trying to retrieve JSON from my server, and display each section in a different headers of a HTML file. I'm not entirely sure how to do that, tried a lot of things, I've managed to get it so the JSON is displayed in Chrome's console log.

Now I don't really understand how I can grab each individual section of JSON to display in a different div. Any help would be appreciated.

HTML:

...

ANSWER

Answered 2017-Sep-25 at 23:55

you arent too far off!

for example:

Source https://stackoverflow.com/questions/46415682

QUESTION

Why does C3p0's ComboPooledDataSource successfully connect to a database, but its clone doesn't?

Asked 2017-Jul-24 at 12:16

In a Tomcat 8.5.15 environment using an Oracle 11 database, I want to implement a data source that handles encrypted passwords in the context.xml. I'm having troubles with that, as described in this StackOverflow question.

In hopes of determining the underlying problem, I simplified the scenario. First, I verified that the C3p0 resource specification worked fine.

...

ANSWER

Answered 2017-Jul-24 at 12:16

These sources (1, 2, 3) discuss this in more detail.

Source https://stackoverflow.com/questions/45242652

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

Vulnerabilities

No vulnerabilities reported

Install JAFFA

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: