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higlass / clodius

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
MIT License
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'Invalid line' message when aggregating bed file #124

Closed rachadele closed 4 years ago

rachadele commented 4 years ago

Hi,

I am trying to use clodius aggregate bedfile on a bed file I made myself, and I keep getting the following message printed to stdout:

Invalid line: 1 15543353    15543354
Invalid line: 1 31706778    31706779

Invalid line: 1 31732787    31732788

Invalid line: 1 31872749    31872750

Invalid line: 1 31920245    31920246

Invalid line: 1 33496638    33496639

Invalid line: 1 47684932    47684933

Invalid line: 1 47695094    47695095

this repeats for every line in my bed file.

does this have to do with the format of my file? I am giving it the --delimiter '\t' option. when I use $'t' as suggested in the higlass manual, clodius is unable to parse my file. I also have a description column in my original bed file, but I removed it to see if it was causing the issue. since I got the error message without the description column, I'm not sure what's causing this.

thx in advance for your help!

pkerpedjiev commented 4 years ago

Would you mind trying --delimiter $'\t'?

Also, would it be possible for you to post a snippet of your file online so I can try to reproduce the issue locally?

rachadele commented 4 years ago

it works now using that delimiter! thanks

pkerpedjiev commented 4 years ago

Great! Sorry about the mistaken docs. I just updated them in the repository and they should be deployed with the next release. Thanks for reporting!