From 823355ec695eff93457360511cc2284791ed6d91 Mon Sep 17 00:00:00 2001 From: Praneeth Date: Mon, 8 Dec 2025 21:38:12 -0800 Subject: [PATCH 1/2] fix: extract_auspice_data saves metadata in tsv format instead of csv format --- barcodeforge/cli.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/barcodeforge/cli.py b/barcodeforge/cli.py index 49bc033..bbe542a 100644 --- a/barcodeforge/cli.py +++ b/barcodeforge/cli.py @@ -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", From be86399c52238f485d5ae15e8408bbe3d9866e67 Mon Sep 17 00:00:00 2001 From: Praneeth Date: Mon, 8 Dec 2025 21:39:06 -0800 Subject: [PATCH 2/2] fix: ref_muts continue _construct_root_sequence even if a sequence is not found --- barcodeforge/ref_muts.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/barcodeforge/ref_muts.py b/barcodeforge/ref_muts.py index ad8912a..3f24aae 100755 --- a/barcodeforge/ref_muts.py +++ b/barcodeforge/ref_muts.py @@ -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: