use a GTF file and a reference FASTA file to index the transcriptome

def index_transcriptome(gtf_file, ref_file, data):
    """
    use a GTF file and a reference FASTA file to index the transcriptome
    """
    gtf_fasta = gtf.gtf_to_fasta(gtf_file, ref_file)
    return build_bwa_index(gtf_fasta, data)