activate_barcode_filter = True
if reference_selected:
set_result_status('Alignment')
if isProtonBlock:
create_index = False
else:
create_index = True
try:
bidirectional = False
alignment.alignment_unmapped_bam(
env['BASECALLER_RESULTS'], basecaller_datasets,
env['ALIGNMENT_RESULTS'], env['realign'],
env['aligner_opts_extra'], env['mark_duplicates'],
create_index, bidirectional, activate_barcode_filter,
env['barcodeInfo'])
add_status("Alignment", 0)
except:
traceback.print_exc()
add_status("Alignment", 1)
printtime("ERROR: Alignment failed")
sys.exit(1)
if isProtonBlock and os.path.exists('/opt/ion/.ion-internal-server'):
printtime("create block level ionstats")
try:
import math
bidirectional = False
##################################################
# Unfiltered BAM
##################################################
if not isProtonBlock:
try:
if os.path.exists(os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed")):
alignment.alignment_unmapped_bam(
os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed"),
os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed"),
env['align_full'],
env['libraryName'],
env['flows'],
env['realign'],
env['aligner_opts_extra'],
env['mark_duplicates'],
bidirectional,
env['sam_parsed'])
#add_status("Alignment", 0)
except:
traceback.print_exc()
#add_status("Alignment", 1)
try:
if os.path.exists(os.path.join(env['BASECALLER_RESULTS'],"unfiltered.trimmed")):
alignment.alignment_unmapped_bam(
os.path.join(env['BASECALLER_RESULTS'],"unfiltered.trimmed"),
os.path.join(env['BASECALLER_RESULTS'],"unfiltered.trimmed"),
set_result_status('Alignment')
if isProtonBlock:
create_index = False
else:
create_index = True
try:
bidirectional = False
alignment.alignment_unmapped_bam(
env['BASECALLER_RESULTS'],
basecaller_datasets,
env['ALIGNMENT_RESULTS'],
env['realign'],
env['aligner_opts_extra'],
env['mark_duplicates'],
create_index,
bidirectional,
activate_barcode_filter,
env['barcodeInfo'])
add_status("Alignment", 0)
except:
traceback.print_exc()
add_status("Alignment", 1)
printtime ("ERROR: Alignment failed")
sys.exit(1)
if isProtonBlock and os.path.exists('/opt/ion/.ion-internal-server'):
##################################################
# Unfiltered BAM
##################################################
if not isProtonBlock:
try:
if os.path.exists(
os.path.join(env['BASECALLER_RESULTS'],
"unfiltered.untrimmed")):
alignment.alignment_unmapped_bam(
os.path.join(env['BASECALLER_RESULTS'],
"unfiltered.untrimmed"),
os.path.join(env['BASECALLER_RESULTS'],
"unfiltered.untrimmed"),
env['align_full'], env['libraryName'],
env['flows'], env['realign'],
env['aligner_opts_extra'], env['mark_duplicates'],
bidirectional, env['sam_parsed'])
#add_status("Alignment", 0)
except:
traceback.print_exc()
#add_status("Alignment", 1)
try:
if os.path.exists(
os.path.join(env['BASECALLER_RESULTS'],
"unfiltered.trimmed")):
alignment.alignment_unmapped_bam(
os.path.join(env['BASECALLER_RESULTS'],