error with the --gff flag

[lyj95618]

Hi,

I am using the newest version 0.0.2 isONclust3 and would like to try the --gff flag and see what is the different between the default and with the --gff flag

here is my command

annotations_gtf=/annotation_files/modified_Homo_sapiens.GRCh38.104.ercc_sirv.sorted.gtf

/tools/isONclust3/target/release/isONclust3 \
--fastq /pacbio_longread/cluster_test/RAGBAP1flnc.fastq \
--mode pacbio \
--outfolder /pacbio_longread/cluster_test/new_isON \
-n 2 --verbose --gff $annotations_gtf

the error I got

thread 'main' panicked at src/gff_handling.rs:152:56:
called `Option::unwrap()` on a `None` value
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Thanks for the help!
Laur

[aljpetri]

Hi thank you for reporting this!
The --gff flag is mainly an experimental flag as we found the outputs of --gff enabled and disabled to be almost identical. In order to run the -gff mode the algorithm additionally requires a reference file (in fasta format) which can be set via --init-cl <path_to_reference.fasta>.