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feat: add support for ignore_unspecified_barcodes in start_protocol helper #1

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feat: add support for ignore_unspecified_barcodes in start_protocol helper #1

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6 changes: 6 additions & 0 deletions python/minknow_api/examples/start_protocol.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,6 +191,11 @@ def parse_args():
action="store_true",
help="bar-code filtering (both ends of a strand must have a matching barcode)",
)
parser.add_argument(
"--ignore-unspecified-barcodes",
action="store_true",
help="ignore unspecified barcodes",
)

# ALIGNMENT ARGUMENTS
parser.add_argument(
Expand Down Expand Up @@ -904,6 +909,7 @@ def _make_request(request_body):
args.barcode_kits,
args.trim_barcodes,
args.barcodes_both_ends,
args.ignore_unspecified_barcodes,
)

if args.alignment_reference:
Expand Down
7 changes: 7 additions & 0 deletions python/minknow_api/tools/protocols.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,6 +192,7 @@ def find_protocol(
"kits",
"trim_barcodes",
"barcodes_both_ends",
"ignore_unspecified_barcodes",
],
)
AlignmentArgs = collections.namedtuple("AlignmentArgs", ["reference_files", "bed_file"])
Expand Down Expand Up @@ -341,6 +342,12 @@ def on_off(value: bool):
"require_barcodes_both_ends="
+ on_off(basecalling.barcoding.barcodes_both_ends)
)
if basecalling.barcoding.ignore_unspecified_barcodes:
# ignore_unspecified_barcodes=on/off
barcoding_args.append(
"ignore_unspecified_barcodes="
+ on_off(basecalling.barcoding.ignore_unspecified_barcodes)
)

protocol_args.extend(["--barcoding"] + barcoding_args)

Expand Down