From f6778a0a11526121ad843456835d6c9b53b17547 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 16 Dec 2025 18:32:13 -0800
Subject: [PATCH 1/3] cmake/FindLIBDEFLATE.cmake: adding

---
 cmake/FindLIBDEFLATE.cmake | 49 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 cmake/FindLIBDEFLATE.cmake

diff --git a/cmake/FindLIBDEFLATE.cmake b/cmake/FindLIBDEFLATE.cmake
new file mode 100644
index 0000000..5584ebc
--- /dev/null
+++ b/cmake/FindLIBDEFLATE.cmake
@@ -0,0 +1,49 @@
+# SPDX-License-Identifier: GPL-3.0-or-later; (c) 2025 Andrew D Smith (author)
+#[=======================================================================[.rst:
+FindLIBDEFLATE
+--------------
+
+Find the native libdeflate includes and library.
+
+#]=======================================================================]
+
+# FindLIBDEFLATE.cmake
+# Custom CMake module to find libdeflate
+
+# Support preference of static libs by adjusting CMAKE_FIND_LIBRARY_SUFFIXES
+# ADS: this is taken from the FindBoost.cmake file
+if(LIBDEFLATE_USE_STATIC_LIBS)
+  set(_libdeflate_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES
+    ${CMAKE_FIND_LIBRARY_SUFFIXES}
+  )
+  if(WIN32)
+    list(INSERT CMAKE_FIND_LIBRARY_SUFFIXES 0 .lib .a)
+  else()
+    set(CMAKE_FIND_LIBRARY_SUFFIXES .a)
+  endif()
+endif()
+
+find_path(LIBDEFLATE_INCLUDE_DIR NAMES libdeflate.h)
+find_library(LIBDEFLATE_LIBRARY NAMES deflate libdeflate)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(LIBDEFLATE
+  REQUIRED_VARS LIBDEFLATE_LIBRARY LIBDEFLATE_INCLUDE_DIR
+  VERSION_VAR LIBDEFLATE_VERSION
+)
+
+if(LIBDEFLATE_FOUND AND NOT TARGET LIBDEFLATE::LIBDEFLATE)
+  add_library(LIBDEFLATE::LIBDEFLATE UNKNOWN IMPORTED)
+  set_target_properties(LIBDEFLATE::LIBDEFLATE PROPERTIES
+    INTERFACE_INCLUDE_DIRECTORIES "${LIBDEFLATE_INCLUDE_DIR}"
+    IMPORTED_LOCATION "${LIBDEFLATE_LIBRARY}"
+  )
+endif()
+
+# Restore the original find library ordering
+# ADS: this is take from the FindBoost.cmake file
+if(LIBDEFLATE_USE_STATIC_LIBS)
+  set(CMAKE_FIND_LIBRARY_SUFFIXES
+    ${_libdeflate_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES}
+  )
+endif()

From 15229ac020f1b56acf06e714b0cb6f96e02deda2 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 16 Dec 2025 18:36:32 -0800
Subject: [PATCH 2/3] src/bamxx: updating submodule

---
 src/bamxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/bamxx b/src/bamxx
index 684f4cd..a15ac9b 160000
--- a/src/bamxx
+++ b/src/bamxx
@@ -1 +1 @@
-Subproject commit 684f4cd6956b384632a4b4778ffc57d256c46a9a
+Subproject commit a15ac9b86d87fea0df8c040ddf75122f7401ec92

From 95ec67c1b0990f5ba6df6b3cb2014dbde663b5d5 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 16 Dec 2025 18:36:57 -0800
Subject: [PATCH 3/3] src/CMakeLists.txt: updating dependencies for targets

---
 src/CMakeLists.txt | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 5fa17b8..403e378 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -13,16 +13,22 @@
 # You should have received a copy of the GNU General Public License along with
 # this program. If not, see <https://www.gnu.org/licenses/>.
 
+if(USE_LIBDEFLATE)
+  find_package(LIBDEFLATE REQUIRED)
+endif()
+
 find_package(HTSLIB REQUIRED)
 find_package(Threads REQUIRED)
+find_package(ZLIB REQUIRED)
 
-if(NOT TARGET bamxx)
-  add_subdirectory(bamxx)
-endif()
 if(NOT TARGET smithlab_cpp)
   add_subdirectory(smithlab_cpp)
 endif()
 
+if(NOT TARGET bamxx)
+  add_subdirectory(bamxx)
+endif()
+
 add_library(abismal_objs OBJECT
   abismal.cpp
   abismalidx.cpp
@@ -33,8 +39,14 @@ target_link_libraries(abismal_objs PUBLIC
   bamxx
   smithlab_cpp
   HTSLIB::HTSLIB
+  ZLIB::ZLIB
   Threads::Threads
 )
+if(USE_LIBDEFLATE)
+  target_link_libraries(abismal_objs PUBLIC
+    LIBDEFLATE::LIBDEFLATE
+  )
+endif()
 # ADS: CMAKE_BINARY_DIR for config.h
 target_include_directories(abismal_objs PUBLIC
   ${CMAKE_CURRENT_SOURCE_DIR}