From 299cc7c85e791802ec89ee8fc8481aa1fb7794db Mon Sep 17 00:00:00 2001
From: Nathan Roach <nathan@fulcrumgenomics.com>
Date: Fri, 30 Dec 2022 10:00:56 -0500
Subject: [PATCH] Adding template coordinate sort order back in for this PR

---
 fgpyo/sam/__init__.py           | 2 ++
 fgpyo/sam/tests/test_builder.py | 9 ++++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/fgpyo/sam/__init__.py b/fgpyo/sam/__init__.py
index fc5502ad..8290916d 100644
--- 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
index b9f89daf..1f235626 100755
--- 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]