gffcompare -d option not having effect

gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

MIT License

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gffcompare -d option not having effect #63

Closed Akazhiel closed 3 years ago

Akazhiel commented 3 years ago

Hello, I've tried running gffcompare with extreme values on the -d parameter and to my surprise all the merged transcripts came out the same size. Is it not having effect or am I misunderstanding the function of this parameter?

gpertea commented 3 years ago

That parameter only controls the tss_id attribute assignments (grouping transcripts by TSS location). It has no influence over the merging of transcripts which is only controlled by structural matching (same intron chain or, in the case of single-exon transcripts, well-bounded overlaps)