MInor fix

genomewalker · Oct 13, 2024 · 0f53317 · 0f53317
1 parent 1d34793
commit 0f53317
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/bam_filter/filter.py b/bam_filter/filter.py
@@ -257,6 +257,7 @@ def filter_references(args):
             sort_by_name=args.sort_by_name,
             min_read_ani=args.min_read_ani,
             disable_sort=args.disable_sort,
+            write_bam=args.bam_filtered is not None,
         )
     else:
         logging.info("Skipping filtering of reference BAM file.")

diff --git a/bam_filter/sam_utils.py b/bam_filter/sam_utils.py
@@ -1067,6 +1067,7 @@ def filter_reference_BAM(
     transform_cov_evenness=False,
     sort_by_name=False,
     disable_sort=False,
+    write_bam=False,
 ):
     """Filter BAM based on certain conditions
 
@@ -1162,7 +1163,7 @@ def filter_reference_BAM(
             sep="\t",
             index=False,
         )
-        if out_files["bam_filtered"] is not None:
+        if write_bam:
             logging.info("Writing filtered BAM file... (be patient)")
             # refs_dict = dict(
             #     zip(df_filtered["reference"], df_filtered["bam_reference_length"])