htsjdk

library5.0.0javamavenunverified

A Java API for reading and writing high-throughput sequencing data in formats like SAM, BAM, VCF, and CRAM.

<dependency>
  <groupId>com.github.samtools</groupId>
  <artifactId>htsjdk</artifactId>
  <version>5.0.0</version>
</dependency>

github ↗homepage ↗docs ↗

INSTALL

IMPORT

SIG · HTSJDK

htsjdk

utilityjavav5.0.0

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

SAMFileReader

✓ htsjdk.samtools.SAMFileReader

Read a BAM file and print read names

import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.SAMRecord; import java.io.File; SAMFileReader reader = new SAMFileReader(new File("input.bam")); for (SAMRecord record : reader) { System.out.println(record.getReadName()); } reader.close();

Debug

Known issues

breakingHTSJDK 5.0.0 changed the default SAMFileReader constructor to require an explicit validation stringency.

fix

Use SAMFileReader(File, ValidationStringency) or set validation stringency explicitly.

affects: >=5.0.0

Upgrade

Version history

5.0.0latest on Maven

Audit

Dependencies

No dependency data recorded yet.

Agent activity

4 hits · last 30 days

node

Resources

githubhttps://github.com/samtools/htsjdk ↗

homepagehttps://samtools.github.io/htsjdk/ ↗

docshttps://appdoc.app/artifact/com.github.samtools/htsjdk/ ↗