Fix preprocess.knockin_handler to correctly identify the flox knock…

…-in sites as deletions not present in the control.

src/DAJIN2/core/preprocess/knockin_handler.py

@@ -11,35 +11,35 @@
 ###########################################################
 # Consider all mutations are possible in the knockin region
 # For large deletion alleles, the deleted sequence becomes the knock-in region, so all mutations within this region are taken into consideration.
-# TODO: Maybe this knock-in consideration isn't necessary?
+# The code identifies the flox knock-in sites as deletions not present in the control.
 ###########################################################
 
 
-def _is_invalid_file(reference: Path, query: Path) -> bool:
-    return query == reference or query.suffix != ".fasta"
+def is_valid_file(control_fasta: Path, knockin_fasta: Path) -> bool:
+    return knockin_fasta != control_fasta and knockin_fasta.suffix == ".fasta"
 
 
-def _get_knockin_loci(reference: Path, query: Path) -> set[int]:
-    alignments = mapping.to_sam(reference, query, preset="splice")
+def get_index_of_knockin_loci(control_fasta: Path, knockin_fasta: Path) -> set[int]:
+    alignments = mapping.to_sam(knockin_fasta, control_fasta, preset="map-ont")
     alignments = [a.split("\t") for a in alignments]
-    alignments_midsv = midsv.transform(alignments, midsv=False, cssplit=True, qscore=False)[0]
+    alignments_midsv = next(iter(midsv.transform(alignments, midsv=False, cssplit=True, qscore=False)))
     cssplits = alignments_midsv["CSSPLIT"].split(",")
 
     return {i for i, cs in enumerate(cssplits) if cs.startswith("-")}
 
 
 def extract_knockin_loci(TEMPDIR: str | Path, SAMPLE_NAME: str) -> None:
-    reference = Path(TEMPDIR, SAMPLE_NAME, "fasta", "control.fasta")
-    for query in Path(TEMPDIR, SAMPLE_NAME, "fasta").iterdir():
-        if _is_invalid_file(reference, query):
+    control_fasta = Path(TEMPDIR, SAMPLE_NAME, "fasta", "control.fasta")
+    for knockin_fasta in Path(TEMPDIR, SAMPLE_NAME, "fasta").iterdir():
+        if not is_valid_file(control_fasta, knockin_fasta):
             continue
 
-        allele = query.stem
+        allele = knockin_fasta.stem
         path_output = Path(TEMPDIR, SAMPLE_NAME, "knockin_loci", f"{allele}.pickle")
         if path_output.exists():
             continue
 
-        knockin_loci = _get_knockin_loci(reference, query)
+        knockin_loci = get_index_of_knockin_loci(control_fasta, knockin_fasta)
 
         with open(path_output, "wb") as p:
             pickle.dump(knockin_loci, p)