fix (fuzzTest): parameters missing for callVariant

uclahs-cds · Jan 19, 2025 · c2da21c · c2da21c
1 parent 78b1335
commit c2da21c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 - Fixed `callVariant` that failed on small circRNA with a lot of variants at the step that creates the cleavage graph. #885
 
+- Fixed `fuzzTest`. Parameters missing for `callVariant`.
+
 ### Changed
 
 - Changed variant IDs for circRNAs to use backsplicing site instead of listing all exons/introns. #878

diff --git a/moPepGen/fake.py b/moPepGen/fake.py
@@ -753,7 +753,7 @@ def fake_genomic_annotation(n_genes:int, chrom:str, min_exons:int, max_exons:int
         )
         gene_start = tx_model.transcript.location.start
         gene_end = tx_model.transcript.location.end
-        loc = FeatureLocation(start=gene_start, end=gene_end, seqname=chrom)
+        loc = FeatureLocation(start=gene_start, end=gene_end, seqname=chrom, strand=strand)
         gene_model = GeneAnnotationModel(
             location=loc, chrom=chrom, transcripts=[tx_id], type='gene',
             attributes=copy.deepcopy(tx_model.transcript.attributes)

diff --git a/moPepGen/util/fuzz_test.py b/moPepGen/util/fuzz_test.py
@@ -630,13 +630,15 @@ def call_variants(self):
         args.min_length = 7
         args.max_length = 25
         args.threads = 1
-        args.max_variants_per_node = 9
-        args.additional_variants_per_misc = 2
+        args.max_variants_per_node = (9, )
+        args.additional_variants_per_misc = (2, )
         args.min_nodes_to_collapse = 30
         args.naa_to_collapse = 5
         args.noncanonical_transcripts = False
         args.invalid_protein_as_noncoding = False
         args.debug_level = 1
+        args.timeout_seconds = 300
+        args.coding_novel_orf = False
         call_variant_peptide(args=args)
 
     def brute_force(self):