if do_composite_alignment or not is_composite:
set_result_status('Alignment')
do_ionstats = True
do_indexing = True
try:
alignment.process_datasets(
dirs,
env['alignmentArgs'],
env['ionstatsArgs'],
env['BASECALLER_RESULTS'],
basecaller_meta_information,
env['libraryKey'],
graph_max_x,
basecaller_datasets,
env['ALIGNMENT_RESULTS'],
env['realign'],
do_ionstats,
env['mark_duplicates'],
do_indexing,
env['barcodeInfo'])
# add_status("Alignment", 0)
except:
traceback.print_exc()
# add_status("Alignment", 1)
else: # is_composite and not do_composite_alignment:
set_result_status('Merge Bam Files')
basecaller_meta_information = None
if reference_selected:
set_result_status('Alignment')
do_ionstats = True
do_indexing = True
alignment.process_datasets(
dirs,
env['alignmentArgs'],
env['ionstatsArgs'],
env['BASECALLER_RESULTS'],
basecaller_meta_information,
env['libraryKey'],
graph_max_x,
basecaller_datasets,
env['ALIGNMENT_RESULTS'],
env['realign'],
do_ionstats,
env['mark_duplicates'],
do_indexing,
env['barcodeInfo'])
'''
### OLD per block processing
if args.do_alignment:
try:
c = open(os.path.join(env['BASECALLER_RESULTS'], "BaseCaller.json"),'r')
basecaller_meta_information = None
if reference_selected:
set_result_status("Alignment")
do_ionstats = True
do_indexing = True
alignment.process_datasets(
dirs,
env["alignmentArgs"],
env["ionstatsArgs"],
env["BASECALLER_RESULTS"],
basecaller_meta_information,
env["libraryKey"],
graph_max_x,
basecaller_datasets,
env["ALIGNMENT_RESULTS"],
env["realign"],
do_ionstats,
env["mark_duplicates"],
do_indexing,
env["barcodeInfo"],
)
"""
### OLD per block processing
if args.do_alignment:
try:
c = open(os.path.join(env['BASECALLER_RESULTS'], "BaseCaller.json"),'r')
basecaller_meta_information = json.load(c)
do_indexing=False
do_ionstats=True
else:
do_indexing=True
do_ionstats=True
try:
blocks=[]
alignment.process_datasets(
blocks,
env['alignmentArgs'],
env['ionstatsArgs'],
env['BASECALLER_RESULTS'],
basecaller_meta_information if do_ionstats_spatial_accounting else None,
env['libraryKey'],
graph_max_x,
basecaller_datasets,
env['ALIGNMENT_RESULTS'],
env['realign'],
do_ionstats,
env['mark_duplicates'],
do_indexing,
env['barcodeInfo'])
add_status("Alignment", 0)
except:
traceback.print_exc()
add_status("Alignment", 1)
printtime ("ERROR: Alignment failed")
sys.exit(1)