def setUpModule():
global annotations, reference_genome, template_metadata, genome_bam_fh, trans_bam_fh, masking
print('setup start')
annotations = load_reference_genes(FULL_REFERENCE_ANNOTATIONS_FILE_JSON)
reference_genome = load_reference_genome(REFERENCE_GENOME_FILE)
template_metadata = load_templates(TEMPLATE_METADATA_FILE)
genome_bam_fh = pysam.AlignmentFile(FULL_BAM_INPUT)
trans_bam_fh = pysam.AlignmentFile(TRANSCRIPTOME_BAM_INPUT)
print('setup loading is complete')
def setUpModule():
global TEMPLATE_METADATA, EXAMPLE_ANNOTATIONS
TEMPLATE_METADATA = load_templates(get_data('cytoBand.txt'))
def setUpModule():
global TEMPLATE_METADATA, EXAMPLE_ANNOTATIONS
TEMPLATE_METADATA = load_templates(TEMPLATE_METADATA_FILE)