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Merged
jkmckenna merged 1 commit into from
Feb 19, 2026
Merged

Update load_adata.py #368

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6 changes: 3 additions & 3 deletions src/smftools/cli/load_adata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -316,7 +316,7 @@ def load_adata_core(cfg, paths: AdataPaths, config_path: str | None = None):
# If the input is a fastq or a directory of fastqs, concatenate them into an unaligned BAM and save the barcode
elif cfg.input_type == "fastq":
# Output file for FASTQ concatenation.
output_bam = load_directory / "canonical_basecalls.bam"
output_bam = bam_outputs_directory / "canonical_basecalls.bam"
if output_bam.exists():
logger.debug("Output BAM already exists")
else:
Expand Down Expand Up @@ -360,9 +360,9 @@ def load_adata_core(cfg, paths: AdataPaths, config_path: str | None = None):
model_basename = str(model_basename).replace(".", "_")
if cfg.smf_modality == "direct":
mod_string = "_".join(cfg.mod_list)
bam = load_directory / f"{model_basename}_{mod_string}_calls"
bam = bam_outputs_directory / f"{model_basename}_{mod_string}_calls"
else:
bam = load_directory / f"{model_basename}_canonical_basecalls"
bam = bam_outputs_directory / f"{model_basename}_canonical_basecalls"
else:
bam_base = cfg.input_data_path.stem
bam = cfg.input_data_path.parent / bam_base
Expand Down