fix test failures: formatting, use of deprecated qname instead of rec…

….query_name

fgpyo/sam/__init__.py

@@ -201,6 +201,7 @@
 ILLUMINA_READ_NAME_DELIMITER: str = ":"
 """Illumina read names are delimited with a colon."""
 
+
 @enum.unique
 class SamFileType(enum.Enum):
     """Enumeration of valid SAM/BAM/CRAM file types.
@@ -946,11 +947,12 @@ class SamOrder(enum.Enum):
     QueryName = "queryname"  #: queryname sorted
     Unknown = "unknown"  # Unknown SAM / BAM / CRAM sort order
 
+
 def extract_umis_from_read_name(
     read_name: str,
     read_name_delimiter: str = ILLUMINA_READ_NAME_DELIMITER,
     umi_delimiter: str = ILLUMINA_UMI_DELIMITER,
-    strict: bool = False
+    strict: bool = False,
 ) -> Optional[str]:
     """Extract UMI(s) from a read name.
     The UMI is expected to be the final component of the read name, delimited by the
@@ -972,11 +974,13 @@ def extract_umis_from_read_name(
     """
     if strict:
         colons = read_name.count(":")
-        if colons == 6: #number of fields is 7
+        if colons == 6:  # number of fields is 7
             return None
         elif colons != 7:
-            raise ValueError(f"Trying to extract UMIs from read with {colons + 1} parts "
-                             f"(7 or 8 expected): {read_name}")
+            raise ValueError(
+                f"Trying to extract UMIs from read with {colons + 1} parts "
+                f"(7 or 8 expected): {read_name}"
+            )
     raw_umi = read_name.split(read_name_delimiter)[-1]
     # Check each UMI individually
     umis = raw_umi.split(umi_delimiter)
@@ -992,6 +996,7 @@ def extract_umis_from_read_name(
         )
     return SAM_UMI_DELIMITER.join(umis)
 
+
 def copy_umi_from_read_name(rec: AlignedSegment, remove_umi: bool = False) -> None:
     """
     Copy a UMI from an alignment's read name to its `RX` SAM tag.
@@ -1008,16 +1013,19 @@ def copy_umi_from_read_name(rec: AlignedSegment, remove_umi: bool = False) -> No
         ValueError: If the record already has a populated `RX` SAM tag.
     """
 
-    umi = extract_umis_from_read_name(read_name=rec.qname,umi_delimiter=ILLUMINA_READ_NAME_DELIMITER)
+    umi = extract_umis_from_read_name(
+        read_name=rec.query_name, umi_delimiter=ILLUMINA_READ_NAME_DELIMITER
+    )
     if not _is_valid_umi(umi):
-            raise ValueError(
-                f"Invalid UMI(s) found in read name: {read_name}",
-            )
+        raise ValueError(
+            f"Invalid UMI(s) found in read name: {rec.query_name}",
+        )
     else:
         rec.set_tag(tag="RX", value=umi, value_type="Z")
         if remove_umi:
-            last_index = rec.qname.rfind(ILLUMINA_READ_NAME_DELIMITER)
-            rec.qname = rec.qname[:last_index] if last_index != -1 else rec.qname
+            last_index = rec.query_name.rfind(ILLUMINA_READ_NAME_DELIMITER)
+            rec.query_name = rec.query_name[:last_index] if last_index != -1 else rec.query_name
+
 
 def _is_valid_umi(umi: str) -> bool:
     """Check whether a UMI is valid.
@@ -1029,4 +1037,4 @@ def _is_valid_umi(umi: str) -> bool:
         True if the UMI is valid, False otherwise.
     """
 
-    return len(umi) > 0 and set(umi).issubset(VALID_UMI_CHARACTERS)
+    return len(umi) > 0 and set(umi).issubset(VALID_UMI_CHARACTERS)