changed the input gtf to output introns to the corrected cds gff #370
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…to incompatibilites with gtftools
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Changed the input gtf to output introns during the making of UJCs to the corrected cds gff due to incompatibilites with gtftools when running SQANTI3 with a fastq. Gtftools needs the exon lines from the gtf to have the "gene_id" flag, but this flag is not added to the corrected.gtf when the mapping step is run internally by SQANTI3. Using the cds version of the corrected gtf solves this.