help for gff format

[dariober]

Hi- First, thanks for developing bioawk!
I noticed that the description of the gff format from bioawk -c help has 10 fields, last two being "group" and "attribute".

bioawk -c help
...
gff:
    1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute 
...

Shouldn't there be 9 fields, where the 9th is either called "attribute" or "group"? For reference: https://www.sanger.ac.uk/resources/software/gff/spec.html#t_2 or http://genome.ucsc.edu/FAQ/FAQformat.html#format3

Dario

[dariober]

Also, if I'm not mistaken the fields "strand" and "filter" (aka frame?) are swapped. I think the fix is in replacing the line in addon.c

{"gff", "seqname", "source", "feature", "start", "end", "score", "filter", "strand", "group", "attribute", NULL}

with

 {"gff", "seqname", "source", "feature", "start", "end", "score", "strand", "filter", "attribute", NULL}

[sahilseth]

@dariober yes, it seems score and filter are swapped. Submit a pull request, maybe?