Thanks for submitting your package. The software is very good. Should a SAF file be created for each bam file or each sample? 

Thank you very much for your kind words.

      You only need a single SAF for a given genome by calling  the following function. This function generate a SAF (simplified annotation format) file for genomic features: genic regions, intergenic regions, exonic regions, intronic regions, rRNA genes, mitochondrial genome, chloroplast genome (only for plants). Any BAM file generated with the same reference genome can be used here. You can also refer to the Vignette for more details.

        saf_list <- get_saf(
        ensdb_sqlite = hs_ensdb_sqlite,
        bamfile = bam_file,
        mitochondrial_genome = "MT"
    )

Haibo