0.4.0 agent working dir

src/smftools/config/experiment_config.py

@@ -713,6 +713,7 @@ class ExperimentConfig:
     # Nanopore specific for basecalling and demultiplexing
     model_dir: Optional[str] = None
     barcode_kit: Optional[str] = None
+    emit_moves: Optional[bool] = True
     model: str = "hac"
     barcode_both_ends: bool = BARCODE_BOTH_ENDS
     trim: bool = TRIM
@@ -1449,6 +1450,7 @@ def from_var_dict(
             mapping_threshold=float(merged.get("mapping_threshold", 0.01)),
             experiment_name=merged.get("experiment_name"),
             model=merged.get("model", "hac"),
+            emit_moves=merged.get("emit_moves", True),
             barcode_both_ends=merged.get("barcode_both_ends", BARCODE_BOTH_ENDS),
             trim=merged.get("trim", TRIM),
             demux_backend=merged.get("demux_backend", "dorado"),

src/smftools/informatics/bam_functions.py

@@ -1042,7 +1042,9 @@ def annotate_umi_tags_in_bam(
                             if umi_values[idx] is None:
                                 umi_values[idx] = extracted
 
-                    if configured_slots and all(umi_values[idx] is not None for idx in configured_slots):
+                    if configured_slots and all(
+                        umi_values[idx] is not None for idx in configured_slots
+                    ):
                         break
             else:
                 for i, ref_side in enumerate(["left", "right"]):

tests/unit/informatics/test_umi_annotation.py

@@ -249,16 +249,21 @@ def test_umi_amplicon_only_from_start(self):
 
     def test_umi_composite_from_start(self, monkeypatch):
         """Extract UMI with composite alignment."""
+
         class _FakeEdlib:
             @staticmethod
             def align(query, target, mode, task, k, additionalEqualities=None):
                 assert mode == "HW"
                 assert task == "path"
                 assert k == 0
                 # Exact match for entire query against target
-                return {"editDistance": 0, "locations": [(0, len(query) - 1)], "cigar": f\"{len(query)}=\"}
+                return {
+                    "editDistance": 0,
+                    "locations": [(0, len(query) - 1)],
+                    "cigar": f"{len(query)}=",
+                }
 
-        monkeypatch.setattr(bam_functions, \"require\", lambda *args, **kwargs: _FakeEdlib())
+        monkeypatch.setattr(bam_functions, "require", lambda *args, **kwargs: _FakeEdlib())
         read = "GTACTGACAATTCCGGAACCTTGGNNNN"
         flanking = FlankingConfig(adapter_side="GTACTGAC", amplicon_side="AACCTTGG")
         umi, start, end = _extract_sequence_with_flanking(