https://github.com/pbenner/jigwig

Java BigWig Reader
https://github.com/pbenner/jigwig

bigwig bigwig-files bioinformatics java java-library

Last synced: 3 months ago
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Java BigWig Reader

• Host: GitHub
• URL: https://github.com/pbenner/jigwig
• Owner: pbenner
• Created: 2017-04-06T16:09:46.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2017-06-21T20:03:07.000Z (almost 8 years ago)
• Last Synced: 2025-01-12T20:21:51.160Z (5 months ago)
• Topics: bigwig, bigwig-files, bioinformatics, java, java-library
• Language: Java
• Homepage:
• Size: 50.8 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        

Library for reading BigWig files (ported from [Gonetics](https://github.com/pbenner/gonetics)).

## Basic Usage

```java

  Path path = Paths.get("test.bw");

  SeekableByteChannel rbc = Files.newByteChannel(path, EnumSet.of(StandardOpenOption.READ));

  BigWigFile bwf = new BigWigFile(rbc);

  BigWigFileIterator it = bwf.query("chr11|chr12", 112643206, 112658727, 0);

  while (it.hasNext()) {

    BigWigFileIteratorType r = it.next();

    BigWigSummaryRecord s = r.getSummary();

    System.out.printf("chrom: %s\n", s.getChromName());

    System.out.printf("from : %d\n", s.getFrom());

    System.out.printf("to   : %d\n", s.getTo());

    System.out.printf("value: %f\n", s.getMean());

    System.out.println();

  }

```