NAME

       flattenGTF  -  Flatten  features  included  in  a  GTF  annotation  and  save the modified
       annotation to a SAF format file.

USAGE

       flattenGTF [options] -a <input_file> -o <output_file>

       ## Mandatory arguments:

       -a <file>
              Name of an annotation file in GTF/GFF format.

       -o <file>
              Name of output file.

       ## Optional arguments:

       -t <string>
              Specify feature type in a GTF annotation. 'exon' by  default.   Features  with  the
              specified feature type are extracted from the annotation for processing.

       -g <string>
              Specify  attribute  type  in  GTF annotation. 'gene_id' by default.  This attribute
              type is used to group features into metafeatures.

       -C     Merging overlapping exons into multiple non-overlapping exons but all the edges are
              kept.