fix: sum_of_base_qualities should be zero when a read has no base qua…

…lities

fgpyo/sam/__init__.py

@@ -849,16 +849,24 @@ def from_read(cls, read: pysam.AlignedSegment) -> List["SupplementaryAlignment"]
 def sum_of_base_qualities(rec: AlignedSegment, min_quality_score: int = 15) -> int:
     """Calculate the sum of base qualities score for an alignment record.
 
-    This function is useful for calculating the "mate score" as implemented in samtools fixmate.
+    This function is useful for calculating the "mate score" as implemented in `samtools fixmate`.
+    Consistently with `samtools fixmate`, this function returns 0 if the record has no base
+    qualities.
 
     Args:
         rec: The alignment record to calculate the sum of base qualities from.
         min_quality_score: The minimum base quality score to use for summation.
 
+    Returns:
+        The sum of base qualities on the input record. 0 if the record has no base qualities.
+
     See:
         [`calc_sum_of_base_qualities()`](https://github.com/samtools/samtools/blob/4f3a7397a1f841020074c0048c503a01a52d5fa2/bam_mate.c#L227-L238)
         [`MD_MIN_QUALITY`](https://github.com/samtools/samtools/blob/4f3a7397a1f841020074c0048c503a01a52d5fa2/bam_mate.c#L42)
     """
+    if rec.query_qualities is None:
+        return 0
+
     score: int = sum(qual for qual in rec.query_qualities if qual >= min_quality_score)
     return score
 

fgpyo/util/inspect.py

@@ -457,7 +457,7 @@ def attr_from(
             # True, because python, so we need to check for that explicitly
             if not set_value and attribute.type is not None and not attribute.type == bool:
                 try:
-                    return_value = attribute.type(str_value)  # type: ignore[operator]
+                    return_value = attribute.type(str_value)
                     set_value = True
                 except (ValueError, TypeError):
                     pass

tests/fgpyo/sam/test_sam.py

@@ -10,6 +10,8 @@
 
 import pysam
 import pytest
+from pysam import AlignedSegment
+from pysam import AlignmentFile
 from pysam import AlignmentHeader
 
 import fgpyo.sam as sam
@@ -616,6 +618,32 @@ def test_sum_of_base_qualities_some_below_minimum() -> None:
     assert sum_of_base_qualities(single, min_quality_score=4) == 9
 
 
+def test_sum_of_base_qualities_unmapped(tmp_path: Path) -> None:
+    builder = SamBuilder(r1_len=5, r2_len=5)
+    single: AlignedSegment = builder.add_single()
+
+    # NB: assigning to `query_qualities` does not affect the cached object returned by the property,
+    # but it does change the underlying attribute used when constructing the string representation
+    single.query_qualities = None
+    record_str = single.to_string()
+
+    bam_path: Path = tmp_path / "no_qualities.bam"
+
+    with bam_path.open("w") as bam_file:
+        bam_file.write(str(builder.header))
+        bam_file.write(f"{record_str}\n")
+
+    with AlignmentFile(str(bam_path)) as bam:
+        record = next(bam)
+
+    # NB: writing to the temp file above is necessary to construct an `AlignedSegment` with no base
+    # qualities, as `SamBuilder` does not currently permit the construction of such records.
+    # TODO simplify this after `SamBuilder` is updated to support this.
+    # https://github.com/fulcrumgenomics/fgpyo/issues/211
+    assert record.query_qualities is None
+    assert sum_of_base_qualities(record) == 0
+
+
 def test_calc_edit_info_no_edits() -> None:
     chrom = "ACGCTAGACTGCTAGCAGCATCTCATAGCACTTCGCGCTATAGCGATATAAATATCGCGATCTAGCG"
     builder = SamBuilder(r1_len=30)