malva | free ALternate-allele detection | Genomics library

by AlgoLab C++ Version: v1.3.1 License: GPL-3.0

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

kandi X-RAY | malva Summary

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

Alignment-free genotyping of a set of known variants (in VCF format) directly from a sample of reads.

Support

Quality

Security

License

Reuse

Support

malva has a low active ecosystem.

It has 7 star(s) with 3 fork(s). There are 7 watchers for this library.

It had no major release in the last 12 months.

There are 2 open issues and 4 have been closed. On average issues are closed in 119 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of malva is v1.3.1

Quality

malva has no bugs reported.

Security

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

License

malva 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.

Reuse

malva releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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 malva

Get all kandi verified functions for this library.

malva Key Features

No Key Features are available at this moment for malva.

malva Examples and Code Snippets

MALVA: genotyping by Mapping-free ALternate-allele detection of known VAriants,Usage

C++

Lines of Code : 43

License : Strong Copyleft (GPL-3.0)

Copy

Usage: malva-geno [-k KMER-SIZE] [-r REF-KMER-SIZE] [-c MAX-COV]   

Arguments:
    -h, --help                        display this help and exit
    -k, --kmer-size                   size of the kmers to index (default:35)
    -r, --ref-kmer-size

Download and installation

C++

Lines of Code : 11

License : Strong Copyleft (GPL-3.0)

Copy

git clone --recursive https://github.com/AlgoLab/malva.git
cd malva

cd sdsl-lite
./install.sh ..
cd ../KMC
make
cd ../htslib
make
cd ..

cd 
make

MALVA: genotyping by Mapping-free ALternate-allele detection of known VAriants,Example

C++

Lines of Code : 6

License : Strong Copyleft (GPL-3.0)

Copy

cd example
tar xvfz data.tar.gz
../MALVA -k 35 -r 43 -b 1 -f EUR_AF chr20.fa chr20.vcf chr20.sample.fa > chr20.genotyped.vcf

mkdir -p kmc_tmp
../KMC/bin/kmc -m4 -k43 -fm chr20.sample.fa kmc.out kmc_tmp
../malva-geno -k 35 -r 43 -b 1 -f EUR_AF chr

Community Discussions

Trending Discussions on malva

Reorganizing dataset for List Length Analysis in R

Plotted mean on boxplot won't appear

Find the solution from a word search game

QUESTION

Reorganizing dataset for List Length Analysis in R

Asked 2020-Mar-18 at 18:48

I have a dataset with oppurtunistic species-observations per square kilometer per year (ranging from 1900 to 2019).

There are 139 different sites (square kilomters) in my dataset. I want to make a dataset where for each species for every year for every site, its presence or absence is stated with 1 or 0.

I think this is the appropriate format for including the length of the species-list per year per site in a GLM, to try and account for repeated visits to sites within years (See Szabo et al. 2010 sci-hub.tw/10.1890/09-0877.1 for application of this method).

Data now looks like:

...

ANSWER

Answered 2020-Mar-18 at 18:48

May be, we can do a complete and create the binary

Source https://stackoverflow.com/questions/60745470

QUESTION

Plotted mean on boxplot won't appear

Asked 2019-Oct-28 at 21:27

I'm trying to add means to a boxplot with points(). The code is working fine, I don't get any errors but the points won't appear.

This is my Code:

...

ANSWER

Answered 2019-Oct-28 at 21:27

in the BN dataframe, the columns are named Bluehstreifen_1 and Bluehstreifen_2, and i am guessing that's BN_1 and BN_2. These columns have NAs, so when you do mean on a column containing NA, it returns NA. Do the following:

Source https://stackoverflow.com/questions/58596919

QUESTION

Find the solution from a word search game

Asked 2018-Nov-19 at 19:22

I have a file with a matrix that is my wordsearch and some words that i need to find in it.

...

ANSWER

Answered 2018-Nov-19 at 18:11

Once you downcased the letter using your code, you can get the result by:

Source https://stackoverflow.com/questions/53379637

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

Vulnerabilities

No vulnerabilities reported

Install malva

MALVA is available on bioconda. will create an environment named malvatest that includes MALVA and its dependencies.
To download and compile the code run the following commands. First clone the repository and cd into it. If you have KMC3, sdsl-lite, and htslib already installed you can skip the following commands. You can now compile MALVA from the root of you local copy of the repository simply by running make.

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: