From 647e65a831bb924ffbbde3975fe7352773bdc99a Mon Sep 17 00:00:00 2001
From: tobiasrausch <rauschtobi@gmail.com>
Date: Thu, 25 Jul 2019 12:47:37 +0200
Subject: [PATCH] sdsl v3

---
 .gitmodules |  8 +++++---
 Makefile    | 11 ++++++-----
 src/sdsl    |  1 -
 src/xxsds   |  1 +
 4 files changed, 12 insertions(+), 9 deletions(-)
 delete mode 160000 src/sdsl
 create mode 160000 src/xxsds

diff --git a/.gitmodules b/.gitmodules
index 369751e..30ccf39 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,6 +1,8 @@
-[submodule "src/sdsl"]
-	path = src/sdsl
-	url = https://github.com/simongog/sdsl-lite.git
 [submodule "src/htslib"]
 	path = src/htslib
 	url = https://github.com/samtools/htslib.git
+	ignore = dirty
+[submodule "src/xxsds"]
+	path = src/xxsds
+	url = https://github.com/xxsds/sdsl-lite.git
+	ignore = dirty
diff --git a/Makefile b/Makefile
index 3b5b3fc..d5cd06f 100644
--- a/Makefile
+++ b/Makefile
@@ -14,8 +14,8 @@ bindir ?= $(exec_prefix)/bin
 
 # Flags
 CXX=g++
-CXXFLAGS += -std=c++11 -isystem ${JLIB} -isystem ${EBROOTHTSLIB} -isystem ${SDSL_ROOT}/include -pedantic -W -Wall -fvisibility=hidden
-LDFLAGS += -L${SDSL_ROOT}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -lsdsl -ldivsufsort -ldivsufsort64 -ldl -L${EBROOTHTSLIB} -L${EBROOTHTSLIB}/lib -lpthread
+CXXFLAGS += -std=c++14 -isystem ${JLIB} -isystem ${EBROOTHTSLIB} -isystem ${SDSL_ROOT}/include -pedantic -W -Wall -fvisibility=hidden
+LDFLAGS += -L${SDSL_ROOT}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -ldl -L${EBROOTHTSLIB} -L${EBROOTHTSLIB}/lib -lpthread
 
 ifeq (${STATIC}, 1)
 	LDFLAGS += -static -static-libgcc -pthread -lhts -lz -llzma -lbz2
@@ -39,7 +39,7 @@ endif
 
 
 # External sources
-SDSLSOURCES = $(wildcard src/sdsl/lib/*.cpp)
+SDSLSOURCES = $(wildcard src/xxsds/lib/*.cpp)
 TRACYSOURCES = $(wildcard src/*.cpp) $(wildcard src/*.h)
 HTSLIBSOURCES = $(wildcard src/htslib/*.c) $(wildcard src/htslib/*.h)
 PBASE=$(shell pwd)
@@ -51,7 +51,7 @@ TARGETS = ${SUBMODULES} ${BUILT_PROGRAMS}
 all:   	$(TARGETS)
 
 .sdsl: $(SDSLSOURCES)
-	if [ -r src/sdsl/install.sh ]; then cd src/sdsl/ && ./install.sh ${PBASE}/src/sdslLite && cd ../../ && touch .sdsl; fi
+	if [ -r src/xxsds/install.sh ]; then cd src/xxsds/ && ./install.sh ${PBASE}/src/sdslLite && cd ../../ && touch .sdsl; fi
 
 .htslib: $(HTSLIBSOURCES)
 	if [ -r src/htslib/Makefile ]; then cd src/htslib && make && make lib-static && cd ../../ && touch .htslib; fi
@@ -65,7 +65,8 @@ install: ${BUILT_PROGRAMS}
 
 clean:
 	if [ -r src/htslib/Makefile ]; then cd src/htslib && make clean; fi
-	if [ -r src/sdsl/install.sh ]; then cd src/sdsl/ && ./uninstall.sh && cd ../../ && rm -rf src/sdslLite/; fi
+	#if [ -r src/xxsds/install.sh ]; then cd src/xxsds/ && ./uninstall.sh ${PBASE}/src/sdslLite && cd ../../ && rm -rf src/sdslLite/; fi
+	if [ -r src/xxsds/install.sh ]; then rm -rf src/sdslLite/; fi
 	rm -f $(TARGETS) $(TARGETS:=.o) ${SUBMODULES}
 
 distclean: clean
diff --git a/src/sdsl b/src/sdsl
deleted file mode 160000
index d52aa9a..0000000
--- a/src/sdsl
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit d52aa9a71513d132e30c09491b5899af449ebb94
diff --git a/src/xxsds b/src/xxsds
new file mode 160000
index 0000000..a654b57
--- /dev/null
+++ b/src/xxsds
@@ -0,0 +1 @@
+Subproject commit a654b574e840cff1db776608b9818655c5f36eee