Juicer Tools Pre: Fixing 4DN DCIC Pairs Format Support
Hey everyone,
We've got a critical issue to dive into today regarding the Juicer Tools Pre and its compatibility with the 4DN DCIC pairs format. It appears that recent versions of the software have broken support for this format due to issues with handling pairs file headers. Let's get into the details and see what's going on.
The Problem: Incorrect Handling of Pairs File Headers
So, here's the deal. Many of us have been loyal users of Juicer Tools for quite some time, relying on it for our Hi-C data analysis. However, it seems that newer versions have introduced a bug that affects the way the software reads standard 4DN DCIC format (pairs) files. Specifically, the problem lies in how Juicer Tools Pre handles the headers of these files.
In older versions, like 1.14.08 and 1.22.01, a standard pairs file with all the correct header lines would work just fine. But in more recent versions, such as 2.16.00 and 2.20.00, users are encountering errors. This is a major headache for those of us working with 4DN data, as it disrupts our established workflows.
To illustrate, here’s an example of a standard pairs file header that used to work:
## pairs format v1.0
#sorted: chr1-chr2-pos1-pos2
#shape: upper triangle
#chromosome: chr1 248956422
#chromosome: chr2 242193529
#chromosome: chr3 198295559
#chromosome: chr4 190214555
#chromosome: chr5 181538259
#chromosome: chr6 170805979
#chromosome: chr7 159345973
#chromosome: chr8 145138636
#chromosome: chr9 138394717
#chromosome: chr10 133797422
#chromosome: chr11 135086622
#chromosome: chr12 133275309
#chromosome: chr13 114364328
#chromosome: chr14 107043718
#chromosome: chr15 101991189
#chromosome: chr16 90338345
#chromosome: chr17 83257441
#chromosome: chr18 80373285
#chromosome: chr19 58617616
#chromosome: chr20 64444167
#chromosome: chr21 46709983
#chromosome: chr22 50818468
#chromosome: chrX 156040895
#chromosome: chrY 57227415
#columns: readID chr1 pos1 chr2 pos2 strand1 strand2
However, in the newer versions, this results in the following error:
WARN [2025-11-17T09:24:11,822] [Globals.java:138] [main] Development mode is enabled
Using 1 CPU thread(s) for primary task
Using 10 CPU thread(s) for secondary task
Not including fragment map
Start preprocess
Writing header
Writing body
java.lang.ArrayIndexOutOfBoundsException: 3
at juicebox.tools.utils.original.mnditerator.ComplexLineParser.generateBasicPair(ComplexLineParser.java:56)
at juicebox.tools.utils.original.mnditerator.MNDFileParser.parseDCICFormat(MNDFileParser.java:118)
at juicebox.tools.utils.original.mnditerator.MNDFileParser.parse(MNDFileParser.java:83)
at juicebox.tools.utils.original.mnditerator.GenericPairIterator.advance(GenericPairIterator.java:56)
at juicebox.tools.utils.original.mnditerator.GenericPairIterator.next(GenericPairIterator.java:46)
at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:603)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:690)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:452)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:176)
at juicebox.tools.HiCTools.main(HiCTools.java:97)
The Temporary Fix
So, what can you do in the meantime? Well, after some digging, it turns out that you can get the newer versions to work by manually removing most of the header lines. You need to be left with only the following:
## pairs format v1.0
#columns: readID chr1 pos1 chr2 pos2 strand1 strand2
This is far from ideal, as it means we're not using the full, standard header as mandated by the 4DN DCIC format. But for now, it's a workaround that allows us to continue using the software.
Why This Matters
Ensuring proper support for standard data formats is crucial for the reproducibility and interoperability of our research. When tools like Juicer Tools Pre fail to correctly parse these formats, it can lead to errors, inconsistencies, and a general lack of confidence in our results. The 4DN DCIC pairs format is widely used in the Hi-C community, and it's essential that software tools accurately handle it.
The Importance of Standard Headers
The header of a pairs file contains critical metadata about the experiment, such as the chromosome lengths, sorting order, and column definitions. This information is used by Juicer Tools Pre to correctly parse the file and perform its analysis. When the header is not properly recognized, the software can misinterpret the data, leading to incorrect results. The full header, as mandated by the standard, is there for a reason. It provides a complete and unambiguous description of the data.
The Impact on Workflows
Many labs have established workflows that rely on the standard 4DN DCIC pairs format. When Juicer Tools Pre breaks support for this format, it can disrupt these workflows and require significant manual intervention. This can be time-consuming and error-prone, as researchers have to manually edit the header of each file before it can be processed. It also adds an extra layer of complexity to the analysis, making it more difficult to reproduce results.
The Call to Action
It would be great if the Juicer Tools team could address this issue and restore proper support for the full 4DN pairs format. This would ensure that the software remains compatible with the latest standards and that users can continue to rely on it for their Hi-C data analysis.
Restoring the full, functional header support as mandated by the standard is essential. This ensures compatibility with the 4DN DCIC pairs format and maintains the integrity of the data analysis pipeline. By addressing this issue, the Juicer Tools team can reaffirm its commitment to the Hi-C community and provide a reliable, user-friendly tool for chromatin interaction analysis.
Ensuring Compatibility with Future Standards
In addition to fixing the current issue, it's important that the Juicer Tools team also considers future standards and updates to the 4DN DCIC pairs format. As the Hi-C field evolves, new metadata and data structures may be introduced, and it's crucial that software tools are able to adapt to these changes. By staying up-to-date with the latest standards, the Juicer Tools team can ensure that their software remains a valuable resource for the Hi-C community.
Let's Get This Fixed!
So, there you have it. A bit of a hiccup in the Juicer Tools Pre world, but hopefully, with a bit of attention, we can get this sorted out. Let's keep the pressure on and ensure that the software we rely on continues to support the standards we need.
Thanks for reading, and let's keep pushing for better tools and better science!
Yours sincerely, Tan
Longzhi Tan (he/him/his) Assistant Professor Department of Neurobiology Stanford University
299 Campus Drive Fairchild Science Building, Room D235 Stanford, CA 94305
Email: tttt@stanford.edu Lab Website: 3dgeno.me