Awesome

About Java Straw

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 <a href="https://github.com/sa501428">Muhammad Saad Shamim</a>. Past contributors include <a href="https://github.com/nchernia">Neva C. Durand</a>, <a href="https://github.com/suhas-rao"> Suhas Rao</a>, and <a href="https://github.com/jrobinso">Jim Robinson</a>.

Questions?

For FAQs, or for asking new questions, please see our forum: <a href="https://aidenlab.org/forum.html"> aidenlab.org/forum.html</a>.

Compiling Jar from IntelliJ

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

Documentation

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