From: "Michael R. Crusoe" <crusoe@debian.org>
Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian package for libdeflate

Forwarded: not-needed
Assisted-By: scaleway/deepseek-v4-flash-0731
---
 Makefile | 21 ++-------------------
 1 file changed, 2 insertions(+), 19 deletions(-)

--- a/Makefile
+++ b/Makefile
@@ -433,7 +433,6 @@ LINLS_DIR:=deps/sublinear-Li-Stephens
 STRUCTURES_DIR:=deps/structures
 BACKWARD_CPP_DIR:=deps/backward-cpp
 DOZEU_DIR:=deps/dozeu
-LIBDEFLATE_DIR:=deps/libdeflate
 LIBVGIO_DIR:=deps/libvgio
 LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
 LIBBDSG_DIR:=deps/libbdsg
@@ -474,7 +473,6 @@ LIB_DEPS += $(LIB_DIR)/libpinchesandcact
 LIB_DEPS += $(LIB_DIR)/libraptor2.a
 LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
 LIB_DEPS += $(LIB_DIR)/libstructures.a
-LIB_DEPS += $(LIB_DIR)/libdeflate.a
 LIB_DEPS += $(LIB_DIR)/libvgio.a
 LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
 LIB_DEPS += $(LIB_DIR)/libbdsg.a
@@ -808,22 +806,6 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLE
 	cd $(LIBHANDLEGRAPH_DIR)/build && $(MAKE) $(FILTER) && $(MAKE) install
 
 
-# On Linux, libdeflate builds a .so.
-# On Mac, it *still* builds an so, which is just a dylib with .so extension.
-# On Mac we need to make sure to set the install name. We do that by renaming to dylib.
-# We don't just leave it as .so because we need to deal with outdated .so files with no paths set.
-$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX): $(LIB_DIR)/libdeflate.a
-	cd $(LIBDEFLATE_DIR) && cp libdeflate.so $(CWD)/$(LIB_DIR)
-	touch $(CWD)/$(LIB_DIR)/libdeflate.so
-ifeq ($(shell uname -s),Darwin)
-	mv $(LIB_DIR)/libdeflate.so $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
-	install_name_tool -id $(CWD)/$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
-endif
-
-$(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDEFLATE_DIR)/lib/*/*.h $(LIBDEFLATE_DIR)/lib/*.c $(LIBDEFLATE_DIR)/lib/*/*.c
-	cd $(LIBDEFLATE_DIR) && V=1 LDFLAGS="$(LDFLAGS) $(LD_RENAMEABLE_FLAGS)" $(MAKE) $(FILTER)
-	cd $(LIBDEFLATE_DIR) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
-
 # We build htslib after libdeflate so it can use libdeflate.
 # We need to do some wizardry to get it to pick up the right build and target system types on modern autotools.
 # We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
@@ -836,7 +818,7 @@ $(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DI
 # headers look for the current HTSlib with <>.
 # Under --always-make, htslib's fallback rule for htscodecs.mk would run and
 # write through configure's symlink into htscodecs_bundled.mk.
-$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc $(LIB_DIR)/libhts%$(SHARED_SUFFIX): $(LIB_DIR)/libdeflate.a $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
+$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc $(LIB_DIR)/libhts%$(SHARED_SUFFIX): $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
 	rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts*
 	cd $(HTSLIB_DIR) && autoreconf -i && autoheader && autoconf || true
 	cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
