hiccupsdiff wrapper arguments error

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Geert Geeven

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Aug 17, 2016, 7:12:34 AM8/17/16
to 3D Genomics
Hi,

I am able to run hiccups on 2 different .hic files, which results in two different loop lists. Then, when I try to run the
hiccupsdiff wrapper :

juicebox hiccupsdiff -m 512 -k KR -f 0.1 S1.hic S2.hic loops1.hiccups loops2.hiccups outputDirectory

I get the following :

 Reading file: S1.hic
HiC file version: 8
Reading file: S2.hic
HiC file version: 8
Exception in thread "main" java.lang.ClassCastException: java.util.HashSet cannot be cast to java.util.List
at juicebox.tools.clt.juicer.HiCCUPSDiff.readJuicerArguments(HiCCUPSDiff.java:103)
at juicebox.tools.clt.JuicerCLT.readArguments(JuicerCLT.java:65)
at juicebox.tools.HiCTools.main(HiCTools.java:76)

somehow it is not able to call the hiccups algorithm with the correct arguments......

Geert

Geert Geeven

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Aug 17, 2016, 7:14:08 AM8/17/16
to 3D Genomics
Btw it doesn't matter if I supply any arguments like -m 512 -k KR -f 0.1 or leave everything to defaults, the error is always the same

Muhammad Saad Shamim

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Aug 17, 2016, 12:43:42 PM8/17/16
to Geert Geeven, 3D Genomics
Hi Geert!

Thank you so much for helping us catch that bug!

We do have automated tests for juicer, but I had forgotten to add hiccups_diff into that.
As such, fixing a recent edge case for a different issue actually affected hiccups_diff.

Part of this bug fix actually propagated from the IGV jar, so I'm running all of our tests 
before updating the jars on the main webpage. I did test hiccups_diff though and
it appears to be working. If you'd like to use the jars now, I've temporarily hosted them here:

Thank you for helping us catch that!
And please let me know if you come across any other issues.

​Best,​

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Geert Geeven

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Aug 18, 2016, 10:44:30 AM8/18/16
to 3D Genomics, geert...@gmail.com
Thanks for the new jar files ! It works now !

Best,

Geert
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