LRA | Long read aligner

by ChaissonLab C++ Version: 1.3.7.2 License: Non-SPDX

X-Ray Key Features Code Snippets(3)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | LRA Summary

LRA is a C++ library. LRA has no bugs, it has no vulnerabilities and it has low support. However LRA has a Non-SPDX License. You can download it from GitHub.

Long read aligner

Support

Quality

Security

License

Reuse

Support

LRA has a low active ecosystem.

It has 108 star(s) with 7 fork(s). There are 9 watchers for this library.

It had no major release in the last 12 months.

There are 13 open issues and 23 have been closed. On average issues are closed in 155 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of LRA is 1.3.7.2

Quality

LRA has 0 bugs and 0 code smells.

Security

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

LRA code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

LRA 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

LRA releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

Top functions reviewed by kandi - BETA

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Get all kandi verified functions for this library.

LRA Key Features

No Key Features are available at this moment for LRA.

LRA Examples and Code Snippets

C++

Lines of Code : 4

License : Non-SPDX (NOASSERTION)

Copy

lra align -CCS/CLR/ONT/CONTIG ref.fa read.fa -t 16 -p s > output.sam  
lra align -CCS/CLR/ONT/CONTIG ref.fa read.fa -t 16 -p p > output.paf  
lra align -CCS/CLR/ONT/CONTIG ref.fa read.fa -t 16 -p b > output.bed

zcat read.fa.gz | lra align -

C++

Lines of Code : 4

License : Non-SPDX (NOASSERTION)

Copy

# index reference genome
lra index -CCS/CLR/ONT/CONTIG ref.fa
# Map sequence to reference
lra align -CCS/CLR/ONT/CONTIG ref.fa read.fa -t 16 -p s > output.sam

C++

Lines of Code : 3

License : Non-SPDX (NOASSERTION)

Copy

lra index -CCS/CLR/ONT/CONTIG ref.fa

lra global -CCS/CLR/ONT/CONTIG ref.fa
lra local -CCS/CLR/ONT/CONTIG ref.fa

Community Discussions

Trending Discussions on LRA

MicroProfile LRA - How to define custom participant URI on a WildFly JEE application?

Quarkus Reactive AMQP client processing in threaded manner

Need to create an SPC chart that updates with new data and uses the last 30 cells as range

Cannot find a physical path bound to logical path matching suffix <> and prefix Coquelicot

Rbar / Rbar_le / coquelicot lemma

Webauthn authentication with Windows Hello via c#

Where is the architecture support implemented in GCC, clang, and/or LLVM in terms of machine code?

SQL - how to get the time by minutes and seconds of each record and then sum the totals

Filtering ls output to only display dirs/files less than certain size

Handsontable update formula variable

QUESTION

MicroProfile LRA - How to define custom participant URI on a WildFly JEE application?

Asked 2022-Apr-12 at 12:03

When MicroProfile LRA coordinator and participants run on different Docker containers, it is needed to define a custom URI for each participant.

Otherwise the LRA coordinator tries to call participant compensate/complete APIs by referring them with "localhost" based URI.

Is it possible, on WildFly environment, to define a custom URI for a participant? And ingeneral is it possible to define a how participants can register with any LRA?

...

ANSWER

Answered 2022-Apr-12 at 12:03

By default, the participant endpoints are derived from the caller information provided in the JAX-RS UriInfo class. This class contains the base URI of the caller of the participant. The idea is that coordinator should be able to call the participant on the same URI as the original request to the participant came in.

I've created a simple docker image https://hub.docker.com/repository/docker/xstefank/uriinfo-wildfly which will on path /uriinfo/ping return the the base URI that will be used for participant URLs.

Calling this locally gives you - Base URI is http://localhost:8080/uriinfo/ which is expected called from the local machine. Deploying this image to OpenShift/Kubernetes and exposing a route for this application gives you Base URI is http://uriinfo-wildfly-testing.6923.rh-us-east-1.openshiftapps.com/uriinfo/. And finally, calling it from a different pod deployed in the same project gives you Base URI is http://uriinfo-wildfly:8080/uriinfo/ which corresponds to the actual calls:

Source https://stackoverflow.com/questions/71838625

QUESTION

Quarkus Reactive AMQP client processing in threaded manner

Asked 2022-Feb-22 at 16:52

I am attempting to use Quarkus' AMQP (reactive-messaging-amqp) extension to decouple work from the original REST request. The idea being the REST call would kick off a long running action and could later come back to get the result.

However, it seems that in my code, Quarkus runs each step in the same thread, completing the work before returning from the original sendNewLRA() call. I would have assumed that the message would be sent through AMQP, thus decoupling the process after the message was sent. Why isn't this the case? I currently don't have any AMQP/messaging specific configuration, and just letting the default run from its own TestContainer (managed by Quarkus)

REST handler:

...

ANSWER

Answered 2022-Feb-22 at 16:52

Found the answer, or at least a fix...

Adding @Blocking to the second step in the messaging chain seems to have decoupled the process:

Source https://stackoverflow.com/questions/71210235

QUESTION

Need to create an SPC chart that updates with new data and uses the last 30 cells as range

Asked 2021-Jul-05 at 07:22

I need some help with Writing some VBA code that produces a line chart. The chart needs to update when new data is added and I also need the displayed range of data to be the last 30 cells of data. I am having to add this to an existing workbook and have been able to write VBA that displays the already existing data on a chart.

what I have already created

...

ANSWER

Answered 2021-Jul-05 at 07:22

Please, test the next code. It will create a chart with series ranges containing the last 30 rows (calculated based on J:J column last row):

Source https://stackoverflow.com/questions/68208762

QUESTION

Cannot find a physical path bound to logical path matching suffix <> and prefix Coquelicot

Asked 2021-Jun-05 at 13:53

I've recently installed Coq version 8.12.2 with opam. I have installed all the packages of Coq using the following command :

opam repo add coq-released https://coq.inria.fr/opam/released

But when I try to compile packages in Coqide, it doesn't recognize coquelicot.

...

ANSWER

Answered 2021-Apr-21 at 11:18

Did you do a

Source https://stackoverflow.com/questions/67183660

QUESTION

Rbar / Rbar_le / coquelicot lemma

Asked 2021-May-08 at 20:17

I am learning Coq via the Coq 8.12.0 reference manual, and have trouble proving the following lemma.

...

ANSWER

Answered 2021-Apr-28 at 06:09

When you entered the tactic right you made a choice in the proof that is not confirmed by the facts in your hypothesis. You should remove this line, and try to find another way to prove your initial conjecture, which really seems provable.

Actually, you are entering into too much detail if you start unfolding the definition of Rle and using destruct. The goal after your ...; intuition is as follows:

Source https://stackoverflow.com/questions/67291367

QUESTION

Webauthn authentication with Windows Hello via c#

Asked 2021-Mar-16 at 05:34

UPDATE: ===========

Having a very similar issue with Elliptical Curve as I did with RSA. VarifyData always returns false.

...

ANSWER

Answered 2021-Mar-09 at 13:32

There may be other issues, but the biggest problem is that you are attempting to verify the signature against the hash of the clientDataJSON. It should actually be the binary concatenation of authenticatorData and the hashed clientDataJSON.

From https://www.w3.org/TR/webauthn/#sctn-verifying-assertion, step 20:

"Using credentialPublicKey, verify that sig is a valid signature over the binary concatenation of authData and hash."

Given what you have, something like this should work:

Source https://stackoverflow.com/questions/66408364

QUESTION

Where is the architecture support implemented in GCC, clang, and/or LLVM in terms of machine code?

Asked 2021-Jan-14 at 21:30

I am looking at this:

...

ANSWER

Answered 2021-Jan-14 at 07:47

Very brief overview for GCC:

GCC's .md machine definition files tell it what instructions are available and what they do, using similar constraint syntax to GNU C inline asm. (GCC doesn't know about machine code, only asm text, that's why it can only output a .s for as to assemble separately.) There are also some C functions that know about generic rules for that architecture, and I guess stuff like register names.

The GCC-internals manual has a section 6.3.9 Anatomy of a Target Back End that documents where the relevant files are in the GCC source tree.

Source https://stackoverflow.com/questions/65714942

QUESTION

SQL - how to get the time by minutes and seconds of each record and then sum the totals

Asked 2020-Sep-23 at 17:06

SQL - how to get the time by minutes and seconds of each record and then sum the totals

look at the images of how it is currently and how I would like it to appear, thanks

...

ANSWER

Answered 2020-Sep-16 at 09:38

Looks like you are stuck on the duration formatting. The @TimeInSeconds variable is a constant (its value does not change after the initial SET) and therefore produces constant results (00:05:10).

The solution below takes the time difference in seconds (datediff(SS, ...)) and adds those seconds to an empty datetime (equal to 1900-01-01 00:00:00.000, abbreviated like 00:00:00 in the code). Converting this back to the type time drops the date part.

Sample data

Source https://stackoverflow.com/questions/63906785

QUESTION

Filtering ls output to only display dirs/files less than certain size

Asked 2020-May-28 at 16:34

I am using ls -lRa to recursively go through my file structure.

However, when I get to large directories it takes a long time to go through them.

How do you filter this ls -lRa command so that if the dir it is ls on is over a certain size then it will just use ls -la and not waste time going recursively through the dir.

I would like to maintain the ls -la format.

Some basic pseudo code might be:

...

ANSWER

Answered 2020-May-28 at 16:34

Obligatory: Don't parse ls

You can use find to count the number of files in a directory, so try something like this:

Source https://stackoverflow.com/questions/62067935

QUESTION

Handsontable update formula variable

Asked 2020-Mar-30 at 09:11

I've got handontable:

...

ANSWER

Answered 2020-Mar-30 at 09:11

Instead of using updateSettings I would use functions from formula plugin.

You may try something like :

Source https://stackoverflow.com/questions/60887575

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

Vulnerabilities

No vulnerabilities reported

Install LRA

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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