'Invalid line' message when aggregating bed file
rachadele opened this issue · 3 comments
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!
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?
it works now using that delimiter! thanks
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!