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fix: fix metadata format and sequence processing #15

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Merged
gp201 merged 2 commits into from
Dec 9, 2025
Merged

fix: fix metadata format and sequence processing #15

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823355e
fix: extract_auspice_data saves metadata in tsv format instead of csv…
gp201 Dec 9, 2025
be86399
fix: ref_muts continue _construct_root_sequence even if a sequence is…
gp201 Dec 9, 2025
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4 changes: 2 additions & 2 deletions barcodeforge/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -295,9 +295,9 @@ def barcode(
@click.option(
"--output_metadata_path",
type=click.Path(),
default="metadata.csv",
default="metadata.tsv",
show_default=True,
help="Path to save the metadata table (CSV format).",
help="Path to save the metadata table (TSV format).",
)
@click.option(
"--output_tree_path",
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2 changes: 1 addition & 1 deletion barcodeforge/ref_muts.py
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Expand Up @@ -174,7 +174,7 @@ def process_and_reroot_lineages(
console.print(
f"[{STYLES['warning']}]Warning: Sample {sample_id} not found in FASTA file. Skipping.[/{STYLES['warning']}]"
)
break
continue
root_seqs.append(_construct_root_sequence(root_muts, seq))

if not root_seqs:
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