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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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Straw successfully dumps data, but juicer_tools.jar fails #266

Closed ArielPaulson closed 2 years ago

ArielPaulson commented 2 years ago

I have several hic files, and when dumping data for certain chromosomes / bin sizes, juicer_tools.jar (even the most recent) will fail, while the equivalent 'straw' command returns the expected data.

For instance this command fails: java -jar juicer_tools.jar dump oe KR $myHicFile 10 10 BP 5000 # 100% "nan"

But this equivalent command succeeds: straw oe KR $myHicFile 10 10 BP 5000 # all normal data

I am using the latest straw build (just a few days ago), versus two different juicer tools versions, both juicer_tools.jar v1.22.01 and feature_tools.jar v2.14.00.

Thanks, Ariel

sa501428 commented 2 years ago

Hey Ariel! Our plan is to deprecate dump in favor of straw, which supports C++, Java, Python, R, and MATLAB. Is there a use case where dump does something that straw cannot do? (if so, we can aim to add that feature to straw)

ArielPaulson commented 2 years ago

Hi Muhammad,

No that I know of. If the plan is to replace dump then everything is ok, just make sure all the wiki instructions get updated!

Thanks, Ariel

From: Muhammad Saad Shamim @.> Sent: Friday, February 11, 2022 2:03 PM To: aidenlab/juicer @.> Cc: Paulson, Ariel @.>; Author @.> Subject: Re: [aidenlab/juicer] Straw successfully dumps data, but juicer_tools.jar fails (Issue #266)

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Hey Ariel! Our plan is to deprecate dump in favor of straw, which supports C++, Java, Python, R, and MATLAB. Is there a use case where dump either outperforms straw or does something that straw cannot do?

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sa501428 commented 2 years ago

Will do, thanks!