scout/server/blueprints/variants/controllers.py
def variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50):
    """Pre-process list of variants."""
    variant_count = variants_query.count()
    skip_count = per_page * max(page - 1, 0)
    more_variants = True if variant_count > (skip_count + per_page) else False
    variant_res = variants_query.skip(skip_count).limit(per_page)

    genome_build = case_obj.get('genome_build', '37')
    if genome_build not in ['37','38']:
        genome_build = '37'

    variants = []
    for variant_obj in variant_res:
        overlapping_svs = [sv for sv in store.overlapping(variant_obj)]
        variant_obj['overlapping'] = overlapping_svs or None
        variants.append(parse_variant(store, institute_obj, case_obj, variant_obj,
                        update=True, genome_build=genome_build))

    return {
        'variants': variants,
        'more_variants': more_variants,
    }
def variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50):
    """Pre-process list of variants."""
    variant_count = variants_query.count()
    skip_count = per_page * max(page - 1, 0)
    more_variants = True if variant_count > (skip_count + per_page) else False
    variant_res = variants_query.skip(skip_count).limit(per_page)

    genome_build = case_obj.get('genome_build', '37')
    if genome_build not in ['37','38']:
        genome_build = '37'

    variants = []
    for variant_obj in variant_res:
        overlapping_svs = [sv for sv in store.overlapping(variant_obj)]
        variant_obj['overlapping'] = overlapping_svs or None
        variants.append(parse_variant(store, institute_obj, case_obj, variant_obj,
                        update=True, genome_build=genome_build))

    return {
        'variants': variants,
        'more_variants': more_variants,
    }
def variants ( store , institute_obj , case_obj , variants_query , page = 1 , per_page = 50 ) : variant_count = variants_query . count ( ) skip_count = per_page * max ( page - 1 , 0 ) more_variants = True if variant_count > ( skip_count + per_page ) else False variant_res = variants_query . skip ( skip_count ) . limit ( per_page ) genome_build = case_obj . get ( 'genome_build' , '37' ) if genome_build not in [ '37' , '38' ] : genome_build = '37' variants = [ ] for variant_obj in variant_res : overlapping_svs = [ sv for sv in store . overlapping ( variant_obj ) ] variant_obj [ 'overlapping' ] = overlapping_svs or None variants . append ( parse_variant ( store , institute_obj , case_obj , variant_obj , update = True , genome_build = genome_build ) ) return { 'variants' : variants , 'more_variants' : more_variants , }
Pre-process list of variants.
Pre - process list of variants .