The '.' class code shown in the .tracking and .combined.gtf files for multiple input files is a result of the transcripts merged there across multiple samples having different relationships (class code) with the reference transcript. Currently gffcompare uses the uninformative "confused" code . but it would be much more informative if a list of the actual codes encountered there should be used instead, e.g. =c if some of the transcripts on that line have code = and others have code c.
The list should be sorted by frequency -- the most frequent class code should be placed first in that concatenated list.
The '.' class code shown in the .tracking and .combined.gtf files for multiple input files is a result of the transcripts merged there across multiple samples having different relationships (class code) with the reference transcript. Currently gffcompare uses the uninformative "confused" code
.
but it would be much more informative if a list of the actual codes encountered there should be used instead, e.g.=c
if some of the transcripts on that line have code=
and others have codec
.The list should be sorted by frequency -- the most frequent class code should be placed first in that concatenated list.