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hictools's Introduction

About HiC Tools

HiC Tools is a software package used to build .hic files. This distribution includes the source code for this set of tools and builds the latest v9 .hic files.

Previously, this software used to be bundled with Juicer Tools in the Juicebox repo.

HiC Tools was originally created by Jim Robinson, Neva C. Durand, and Erez Lieberman Aiden. It has been substantially upgraded and improved by Muhammad S Shamim, Suhas S.P. Rao, and many additional contributors.

If you use HiC Tools in your research, please cite: Neva C. Durand, Muhammad S. Shamim, Ido Machol, Suhas S. P. Rao, Miriam H. Huntley, Eric S. Lander, and Erez Lieberman Aiden. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments." Cell Systems 3(1), 2016.

Questions?

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

IntelliJ Setup

Use 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.
  • Then go to Run -> Edit Configurations.
  • With the + sign, add Application.
  • You'll create one of these for HiC Tools.
  • Set the main class by clicking the little ... button next to the text box for main class
  • HiCTools.java is the main method class.
  • Under VM Options, set -Xmx2000m
  • The Xmx2000m flag sets the maximum memory heap size to 2GB. Depending on your computer you might want more or less. Some tools will break if there's not enough memory and the file is too large, but don't worry about that for development; 2GB should be fine.
  • 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.

Hardware and Software Requirements

The minimum software requirement to run Juicebox is a working Java installation (version > 1.8) on Windows, Linux, and Mac OSX. We recommend using the latest Java version available, but please do not use the Java Beta Version. Minimum system requirements for running Java can be found at https://java.com/en/download/help/sysreq.xml. To download and install the latest Java Runtime Environment (JRE), please go to https://www.java.com/download.

Documentation

We have extensive documentation for how to use HiC Tools at https://github.com/aidenlab/juicer/wiki.

hictools's People

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hictools's Issues

[BUG] does not accept proper pairix format

Describe the bug
When giving pre a file in pairix format, it fails to parse the file and throws an exception. To make it accept pairix format, you have to remove some header lines that it does not expect, despite these header lines being officially part of the pairix specification.

To Reproduce
Steps to reproduce the behavior:

  1. Find a valid pairix format file, containing header lines starting with ## pairs, #shape, #chromsize, and #columns, as specified in https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md
  2. Run hic_tools pre with this file as input:
java -Xmx36G -jar /path/to/hic_tools.jar pairix_file.pairs outfile.hic chrom.sizes

This results in the following error:

java.lang.ArrayIndexOutOfBoundsException: 3
        at hic.tools.utils.iterators.mnd.ComplexLineParser.generateBasicPair(ComplexLineParser.java:56)
        at hic.tools.utils.iterators.mnd.MNDFileParser.parseDCICFormat(MNDFileParser.java:118)
        at hic.tools.utils.iterators.mnd.MNDFileParser.parse(MNDFileParser.java:83)
        at hic.tools.utils.iterators.mnd.GenericPairIterator.advance(GenericPairIterator.java:56)
        at hic.tools.utils.iterators.mnd.GenericPairIterator.next(GenericPairIterator.java:46)
        at hic.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:88)
        at hic.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:114)
        at hic.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:54)
        at hic.tools.clt.old.PreProcessing.run(PreProcessing.java:149)
        at hic.tools.HiCTools.main(HiCTools.java:83)

It appears to be trying to parse one of the header lines as if it is not a header line. To fix, I removed all header lines except those starting with ## pairs and #columns and it worked fine.

Expected behavior
The program should not crash on validly-formatted pairix format input.

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