add option to assemble transfrags in the combined.gtf output

gpertea / gffcompare

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

MIT License

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add option to assemble transfrags in the combined.gtf output #79

Open gpertea opened 1 year ago

gpertea commented 1 year ago

A new option (e.g. --assemble) should allow gffcompare to extend the transfrag-merging ability in the resulting combined.gtf output. Intron-compatible transfrags could be merged based on at least n>=1 matching introns, where the user can control the n value.

This is meant to be a more conservative alternative to stringtie --merge.

gpertea commented 1 year ago

[ ] implement a greedy algorithm to iteratively assemble intron-compatible transfrags in decreasing order of their "structural overlap score"
[ ] when a reference annotation is given (-r), implement ref locus boundary check / gene fusion-prevention option - to prevent the resulting assemblies from fusion-bridging multiple reference loci during the iterative extension-assembly process (unless the reference loci already overlap, e.g. PCDH genes)