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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 Muhammad Saad Shamim. Past contributors include Neva C. Durand, Suhas Rao, and Jim Robinson.

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Questions?

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

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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

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Documentation

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