Adding template coordinate sort order back in for this PR

fulcrumgenomics · Dec 30, 2022 · 299cc7c · 299cc7c
1 parent 45ad823
commit 299cc7c
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Showing 2 changed files with 10 additions and 1 deletion.
diff --git a/fgpyo/sam/__init__.py b/fgpyo/sam/__init__.py
@@ -849,4 +849,6 @@ class SamOrder(enum.Enum):
     Unsorted = "unsorted"  #: the SAM / BAM / CRAM is unsorted
     Coordinate = "coordinate"  #: coordinate sorted
     QueryName = "queryname"  #: queryname sorted
+    TemplateCoordinate = "unsorted"  #: the sort order (@HD SO) is unsorted, the group order (GO)
+    #: is query, and the sub-sort (SS) is template-coordinate
     Unknown = "unknown"  # Unknown SAM / BAM / CRAM sort order
diff --git a/fgpyo/sam/tests/test_builder.py b/fgpyo/sam/tests/test_builder.py
@@ -240,8 +240,15 @@ def make_sort_order_builder(tmp_path: Path, sort_order: SamOrder) -> Path:
         (SamOrder.QueryName, ["test1", "test2", "test3", "test4"]),
         (SamOrder.Unsorted, ["test3", "test2", "test1", "test4"]),
         (None, ["test3", "test2", "test1", "test4"]),
+        (SamOrder.TemplateCoordinate, ["test3", "test2", "test1", "test4"]),
+    ],
+    ids=[
+        "Coordinate sorting",
+        "Query name sorting",
+        "Unsorted output",
+        "Unsorted output - None",
+        "Template Coordinate",
     ],
-    ids=["Coordinate sorting", "Query name sorting", "Unsorted output", "Unsorted output - None"],
 )
 def test_sort_types(
     tmp_path: Path, sort_order: Optional[SamOrder], expected_name_order: List[str]