Java Straw is a library for quickly reading data from the HiC file format, to be used directly in code without dumping data to a local file.

Here's a detailed example of how to use Java-Straw: AnnotatedExample.java

Ongoing development work is carried out by Muhammad Saad Shamim. Past contributors include Neva C. Durand, Suhas Rao, and Jim Robinson.

For FAQs, or for asking new questions, please see our forum: aidenlab.org/forum.html.

Precompiled jars are available under Github Releases. We recommend using the latest version.

You can build jars from source code using IntelliJ IDEA (Community edition - free)

To set up in IDEA, have the Java SDK installed then you'll point to it (IntelliJ has lots of documentation on this sort of thing).

• Then go to VCS -> checkout from version control.
• You'll need to do is be sure *.sizes is included as a file to be copied over to the class files. Set this up via IntelliJ Preferences -> Compiler. Add ?*.sizes to the list of Resource Patterns.
• One last note: be sure to Commit and Push when you commit files, it's hidden in the dropdown menu button in the commit window.
• Compiling the code should automatically build the jar under out/artifacts/java_straw_jar

We have documentation for how to use Java Straw at https://github.com/aidenlab/java-straw/wiki.