R script reading of GFF files
In certain data sets, the error below occurs.
[1] "Read in gff3 annotation file"
Read 254171 records
Error in validObject(.Object) :
invalid class "Genome_intervals_stranded" object: The 'annotation' slot should have a column named 'inter_base' that is logical and does not contain missing values.
Calls: readGff3 ... eval -> eval -> .nextMethod -> initMatrix -> validObject
In addition: Warning message:
In readGff3(annot_file, isRightOpen = TRUE) :
'readGff3' has changed to closed interval conventions!
Use 'isRightOpen=TRUE' to restore the previous behavior
that allowed for zero-length features. Alternatively, use
the readZeroLengthFeaturesGff3 function instead.
You can turn off this warning by setting 'quiet=TRUE'
Execution halted
Need to handle these cases appropriately so that the pipeline doesn't break for this error.