Reintroducing lz4 because Debian recently dropped lz4frames.h and rel…

…ated

functions from the liblz4-dev package(!?)

.gitmodules

@@ -1,3 +1,12 @@
 [submodule "htslib"]
 	path = htslib
 	url = https://github.com/lomereiter/htslib.git
+[submodule "undeaD"]
+	path = undeaD
+	url = https://github.com/dlang/undeaD
+[submodule "BioD"]
+	path = BioD
+	url = https://github.com/biod/BioD.git
+[submodule "lz4"]
+	path = lz4
+	url = https://github.com/lz4/lz4.git

.travis.yml

@@ -1,5 +1,22 @@
 language: d
 d:
   - ldc
+matrix:
+  # OSX testing is under development
+  allow_failures:
+    - os: osx
+  include:
+    - os: linux
+      compiler: gcc
+      addons:
+        apt:
+          packages:
+            # Our dev environment is a more recent GNU C++
+            # note that Debian liblz4-dev no longer supports LZ4 frames
+            # - liblz4-dev
+            - shunit2
+    - os: osx
+      compiler: clang
 script:
   - make
+  - make test

Makefile

@@ -18,7 +18,7 @@ DFLAGS      = -wi -I. -IBioD -IundeaD/src -g
 
 DLIBS       = $(LIBRARY_PATH)/libphobos2-ldc.a $(LIBRARY_PATH)/libdruntime-ldc.a
 DLIBS_DEBUG = $(LIBRARY_PATH)/libphobos2-ldc-debug.a $(LIBRARY_PATH)/libdruntime-ldc-debug.a
-LIBS        = htslib/libhts.a -L-llz4 -L-L$(LIBRARY_PATH) -L-lrt -L-lpthread -L-lm
+LIBS        = htslib/libhts.a lz4/lib/liblz4.a -L-L$(LIBRARY_PATH) -L-lrt -L-lpthread -L-lm
 LIBS_STATIC = $(LIBRARY_PATH)/libc.a $(DLIBS) htslib/libhts.a $(LIBRARY_PATH)/liblz4.a
 SRC         = $(wildcard main.d utils/*.d thirdparty/*.d cram/*.d) $(wildcard undeaD/src/undead/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio2/*.d BioD/bio2/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
 OBJ         = $(SRC:.d=.o) utils/ldc_version_info_.o
@@ -40,6 +40,11 @@ pgo-static:                        DFLAGS += -fprofile-instr-use=profile.data
 
 all: release
 
+lz4-static: lz4/lib/liblz4.a
+
+lz4/lib/liblz4.a: lz4/lib/lz4.c lz4/lib/lz4hc.c lz4/lib/lz4frame.c lz4/lib/xxhash.c
+	cd lz4/lib && gcc -O3 -c lz4.c lz4hc.c lz4frame.c xxhash.c && $(AR) rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o
+
 htslib-static:
 	cd htslib && $(MAKE)
 
@@ -50,7 +55,7 @@ ldc-version-info:
 utils/ldc_version_info_.o: ldc-version-info
 	$(D_COMPILER) $(DFLAGS) -c utils/ldc_version_info_.d -od=$(dir $@)
 
-build-setup: htslib-static ldc-version-info
+build-setup: lz4-static htslib-static ldc-version-info
 	mkdir -p bin/
 
 default debug release static: $(OUT)