htsjdk | Java API for high-throughput sequencing data | Genomics library

by samtools Java Version: 3.0.5 License: No License

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | htsjdk Summary

htsjdk is a Java library typically used in Artificial Intelligence, Genomics applications. htsjdk has build file available and it has low support. However htsjdk has 208 bugs and it has 3 vulnerabilities. You can download it from GitHub, Maven.

HTSJDK is now built using gradle. A wrapper script (gradlew) is included which will download the appropriate version of gradle on the first invocation.

Support

Quality

Security

License

Reuse

Support

htsjdk has a low active ecosystem.

It has 260 star(s) with 248 fork(s). There are 50 watchers for this library.

It had no major release in the last 12 months.

There are 252 open issues and 325 have been closed. On average issues are closed in 599 days. There are 43 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of htsjdk is 3.0.5

Quality

htsjdk has 208 bugs (44 blocker, 9 critical, 72 major, 83 minor) and 4478 code smells.

Security

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

htsjdk code analysis shows 3 unresolved vulnerabilities (0 blocker, 2 critical, 0 major, 1 minor).

There are 61 security hotspots that need review.

License

htsjdk 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

htsjdk releases are available to install and integrate.

Deployable package is available in Maven.

Build file is available. You can build the component from source.

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

htsjdk saves you 97619 person hours of effort in developing the same functionality from scratch.

It has 105687 lines of code, 9911 functions and 982 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

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

Create a map of the generated genotypes
Utility function to parse the GL formatted GL format strings in VCF format
Decode a comma - separated list of integers
Parse genotype alleles from VCF string
Produce reference bases from a SAMRecord
Get the value of the specified attribute
Get attribute by tag
Replies the span for the specified bin
Computes the span between the start and endPos
Combines multiple program groups into a single list
Main entry point
Capture the locator information contained within the given SAMRecord
Merges a collection of VCF headers to a set of VCF headers
Creates an index file from the input stream
Reads the next record from the input stream
Returns a deep copy of this SAMRecord
Parses the given value line and returns a map of tags
Gets a TIntv from a string
Extract other canonical alignments from a SAM record
Internal read method
Merges two SAMSequences
Write the reference to the BAMIndexContent
Adds an unmapped pair
Calculates the md and NM tags
This method is used to calculate the distance between two strings
Read the header

Get all kandi verified functions for this library.

htsjdk Key Features

No Key Features are available at this moment for htsjdk.

htsjdk Examples and Code Snippets

No Code Snippets are available at this moment for htsjdk.

Community Discussions

Trending Discussions on htsjdk

gradle build broken after dependency update

QUESTION

gradle build broken after dependency update

Asked 2020-Aug-24 at 08:01

I use gradle to build a java project (ASCIIGenome).

One of the dependencies of ASCIIGenome is a repository on github (htsjdk, as you can see is a fork with some changes of mine). The ASCIIGenome project builds fine if I use this commit of htsjdk in build.gradle:

...

ANSWER

Answered 2020-Aug-24 at 08:01

It turns out there is a bug in the .gitignore repository of htsjdk that caused some files to be ignored so the htsjdk dependency was broken. Fixing .gitignore fixed my problem.

Source https://stackoverflow.com/questions/63539191

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

Vulnerabilities

No vulnerabilities reported

Install htsjdk

You can download it from GitHub, Maven.
You can use htsjdk 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 htsjdk 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

API documentation for all versions of HTSJDK since 1.128 are available through javadoc.io. If you believe you have found a bug or have an issue with the library please a) search the open and recently closed issues to ensure it has not already been reported, then b) log an issue. The project has a gitter chat room if you would like to chat with the developers and others involved in the project. To receive announcements of releases and other significant project news please subscribe to the htsjdk-announce google group.

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