Sascha Steinbiss
Sascha Steinbiss
Can you share your bed file or part of it so we can use it to reproduce the issue? Thanks! It looks like there is a problem with the formatting...
The issue remains, since I do not remember receiving an example file. @SSPuliasis can you provide a (minimal?) example file that would allow me to reproduce the issue? Feel free...
Thanks, I'll take a look.
Looks like your BED file has 14 columns while the spec (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) only describes 12: ``` chr1 65418 71585 A0A2U3U0J3 0 + 65564 70007 255,0,0 3 15,54,2549 0,101,3618 A0A2U3U0J3 M1-K3,V4-F326...
As a workaround, you can simply cut off the superfluous fields and then pass the result to `gt bed_to_gff3`: ``` $ cat sample_bed_file.txt | cut -f1-12 | gt bed_to_gff3 ##gff-version...
I see... Weird that they simply extend the format and potentially break parsers... :/ I'm a fan of 'strict by default' parsers, but with the "be liberal with what you...
Can we consider this done, btw?
Tagging this as "enhancement" as there is now only a feature request to ignore BED columns beyond the 12th.
Due to this problem the offending test has been currently disabled on Mac OS X. It must be re-enabled when this problem is fixed.
Ok. Do you think we should close this issue or keep it around for reference?