harpy/bin/depth_windows.py (3)

26-28: Good addition of zero check, but needs error logging.

The protection against division by zero is good, but we should log when we skip windows to help diagnose issues.

 if WINSIZE > 0:
     depth = _SUM / WINSIZE
     print(f"{LAST_CONTIG}\t{POSITION}\t{depth}", file = sys.stdout)
+else:
+    print(f"Warning: Skipping window for {LAST_CONTIG} due to zero window size", file=sys.stderr)

---

Line range hint 7-11: Add input validation for windowsize.

The script should validate that the windowsize argument is positive before processing any data.

 parser.add_argument('windowsize', type= int, help = "The window size to use to calcualte mean depth over (non-overlapping)")

 args = parser.parse_args()
+if args.windowsize <= 0:
+    print("Error: Window size must be greater than zero", file=sys.stderr)
+    sys.exit(1)
+
 _SUM = 0

---

Line range hint 1-44: Consider adding error handling and logging.

The script would benefit from proper error handling and logging to help diagnose issues in production:

1. Add try-except blocks around file operations
2. Use Python's logging module
3. Add progress indicators for long-running operations

Would you like me to provide an example implementation with these improvements?

harpy/bin/assign_mi.py (1)

86-89: Consider defining the default BX value as a constant.

The implementation correctly removes MI and DI tags while adding a default BX tag. However, the hardcoded value "A00C00B00D00" could be defined as a constant at the module level for better maintainability.

Consider adding this at the top of the file:

+# Default BX tag value for records with missing BX tags
+DEFAULT_BX_VALUE = "A00C00B00D00"

Then update the write_missingbx function:

-    tags.append(("BX", "A00C00B00D00"))
+    tags.append(("BX", DEFAULT_BX_VALUE))

harpy/bin/deconvolve_alignments.py (3)

25-25: Avoid using 'input' as an argument name to prevent shadowing

Using 'input' as the argument name shadows the built-in input() function in Python, which might lead to unexpected behavior.

Consider renaming the argument to 'input_file'.

Apply this diff:

-parser.add_argument('input', help = "Input coordinate-sorted bam/sam file")
+parser.add_argument('input_file', help = "Input coordinate-sorted bam/sam file")

...

-bam_input = args.input
+bam_input = args.input_file

---

52-71: Resolve contradiction regarding MI tag handling in write_invalidbx

The docstring states that the function keeps the existing MI tag if present, but the comment contradicts this by stating it will not keep an existing MI tag. Please ensure the documentation and code behavior are consistent.

Update the docstring or adjust the code to accurately reflect the function's behavior.

---

101-102: Simplify nested if statements by combining them

To improve code readability, you can combine the nested if statements into a single condition using and.

Apply this diff to simplify the code:

-if bam_input.lower().endswith(".bam"):
-    if not os.path.exists(bam_input + ".bai"):
+if bam_input.lower().endswith(".bam") and not os.path.exists(bam_input + ".bai"):

🧰 Tools

🪛 Ruff

101-102: Use a single if statement instead of nested if statements

Combine if statements using and

(SIM102)

Configuration used: CodeRabbit UI
Review profile: CHILL

#!/bin/bash
# Search for the molecule_coverage rule and its dependencies
rg -l "molecule_coverage" | while read -r file; do
  echo "=== $file ==="
  rg "rule molecule_coverage" "$file" -A 10
done

# Search for potential division operations in related files
rg "ZeroDivisionError|/ 0|\b/\s*0\b" 

#!/bin/bash
# Search for code that relies on MI tags
rg -l "MI" | grep -v "assign_mi.py" | while read -r file; do
  echo "=== $file ==="
  rg "get_tag\(['\"]MI['\"]" "$file" -A 2
done

#!/bin/bash
# Let's check for MI tag usage in molecule_coverage.py since it's related to the divide-by-zero error
echo "=== molecule_coverage.py content ==="
cat harpy/bin/molecule_coverage.py

# Also check for any other files that might process MI tags
echo -e "\n=== Files referencing MI tags ==="
rg -l "MI" --type py

# Check specific MI tag processing
echo -e "\n=== MI tag processing in Python files ==="
rg "MI" --type py -B2 -A2