Removing CRAM support

.guix-build

@@ -0,0 +1,3 @@
+# This command creates a build container for Sambamba using GNU Guix
+
+guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim zlib

INSTALL.md

@@ -3,12 +3,8 @@
 ## Sambamba dependencies
 
 * D compiler (ldc)
-* BioD (git submodule)
-* gcc tool chain (for htslib and lz4)
-* htslib (git submodule)
-* undeaD (git submodule)
+* gcc tool chain (for lz4)
 * libz
-* liblz4
 
 ## Install Sambamba from source
 
@@ -22,13 +18,20 @@ and run our development setup (gold was added lately by ldc)
 
     guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim
     make clean
-    make -j 4
-    make check
+    make -f Makefile.guix -j 4
+    make -f Makefile.guix check
 
-this way all dependencies are isolated.
+this way all dependencies are isolated. To create a static release use
 
-## Build Sambamba with Debian
+    make static
 
-Make sure the environment is minimal with something like
+## Development
 
-    env -i /bin/bash --login --noprofile --norc
+We use GNU Guix containers for development. Install Guix and run a build
+container with
+
+    . .guix-build
+    make -f Makefile.guix
+    make -f Makefile.guix check
+
+Note that this also works in the emacs shell.

Makefile

@@ -32,13 +32,13 @@ DFLAGS      = -wi -I. -IBioD -g -J.
 
 DLIBS       = $(LIBRARY_PATH)/libphobos2-ldc.a $(LIBRARY_PATH)/libdruntime-ldc.a
 DLIBS_DEBUG = $(LIBRARY_PATH)/libphobos2-ldc-debug.a $(LIBRARY_PATH)/libdruntime-ldc-debug.a
-LIBS        = htslib/libhts.a lz4/lib/liblz4.a -L-L$(LIBRARY_PATH) -L-lpthread -L-lm -L-lz
-LIBS_STATIC = $(LIBRARY_PATH)/libc.a $(DLIBS) htslib/libhts.a $(LIBRARY_PATH)/liblz4.a -L-lz
-SRC         = utils/ldc_version_info_.d utils/lz4.d utils/strip_bcf_header.d $(sort $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d)) utils/version_.d $(sort $(wildcard thirdparty/*.d cram/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d))
+LIBS        = lz4/lib/liblz4.a -L-L$(LIBRARY_PATH) -L-lpthread -L-lm -L-lz
+LIBS_STATIC = $(LIBRARY_PATH)/libc.a $(DLIBS) $(LIBRARY_PATH)/liblz4.a -L-lz
+SRC         = utils/ldc_version_info_.d utils/lz4.d utils/strip_bcf_header.d $(sort $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d)) utils/version_.d $(sort $(wildcard thirdparty/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d))
 OBJ         = $(SRC:.d=.o)
 OUT         = bin/sambamba-$(shell cat VERSION)
 
-STATIC_LIB_PATH=-Lhtslib -Llz4
+STATIC_LIB_PATH=-Llz4
 
 .PHONY: all debug release static clean test
 
@@ -61,16 +61,13 @@ 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) -j8
-
 utils/ldc_version_info_.d:
 	python3 ./gen_ldc_version_info.py $(shell which ldmd2) > utils/ldc_version_info_.d
 	cat utils/ldc_version_info_.d
 
 ldc_version_info: utils/ldc_version_info_.d
 
-build-setup: ldc_version_info lz4-static htslib-static
+build-setup: ldc_version_info lz4-static
 	mkdir -p bin/
 
 default debug release static: $(OUT)
@@ -115,7 +112,6 @@ install:
 	install -m 0755 bin/sambamba $(prefix)/bin
 
 clean: clean-d
-	cd htslib ; $(MAKE) clean
 	rm lz4/lib/*.[oa]
 	rm -f profile.data
 	rm -f profile.raw

Makefile.guix

@@ -27,11 +27,10 @@ DFLAGS = -wi -I. -I$(BIOD_PATH) -J.
 # DLIBS_DEBUG = -debuglib=phobos2-ldc-debug-shared,druntime-ldc-debug-shared -link-debuglib -L-lphobos2-ldc-debug-shared -L-ldruntime-ldc-debug-shared
 # RPATH  = -L--rpath=$(dir $(realpath $(LDC_LIB_PATH)/libz.so)):$(dir $(realpath $(LDC_LIB_PATH)/liblz4.so))
 RPATH = -L--rpath=$(LIBRARY_PATH)
-LIBS   = htslib/libhts.a -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz lz4/lib/liblz4.a
+LIBS   = -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz lz4/lib/liblz4.a
 
-# LIBS   = htslib/libhts.a -L-lrt -L-lpthread -L-lm -L-lz -L-llz4
-LIBS_STATIC = $(DLIBS) htslib/libhts.a lz4/lib/liblz4.a
-SRC         = $(wildcard main.d utils/*.d thirdparty/*.d cram/*.d) $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d BioD/bio/*/*/*/*/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
+LIBS_STATIC = $(DLIBS) lz4/lib/liblz4.a
+SRC         = $(wildcard main.d utils/*.d thirdparty/*.d) $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d BioD/bio/*/*/*/*/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
 OBJ    = $(SRC:.d=.o) utils/ldc_version_info_.o
 OUT    = bin/sambamba-$(shell cat VERSION)
 static: OUT += -static
@@ -77,7 +76,7 @@ lz4/lib/liblz4.a: lz4/lib/lz4.c lz4/lib/lz4hc.c lz4/lib/lz4frame.c lz4/lib/xxhas
 
 lz4-static: lz4/lib/liblz4.a
 
-build-setup: ldc_version_info lz4-static htslib-static
+build-setup: ldc_version_info lz4-static
 	mkdir -p bin/
 
 # utils/ldc_version_info_.o: utils/ldc_version_info_.d
@@ -93,7 +92,6 @@ debug profile release: lz4-static
 
 # ---- Link step
 $(OUT): $(OBJ)
-	cd htslib && $(MAKE) -j 4
 	mkdir -p bin/
 	$(D_COMPILER) $(DFLAGS) -of=$(OUT) $(OBJ) $(LIBS)
 
@@ -115,7 +113,6 @@ install:
 	install -m 0755 bin/sambamba $(prefix)/bin
 
 clean-c:
-	cd htslib ; make clean
 	rm -v lz4/lib/*.[oa]
 
 clean-d:

RELEASE-NOTES.md

@@ -1,3 +1,14 @@
+
+## ChangeLog v0.8.0 (2020??)
+
+Maintainance release and bug fixes: this is a special release where we
+removed all CRAM support. The added value of CRAM in sambamba was
+limited because it was using essentially the same htslib backend as
+samtools. Removing the htslib dependency removes one maintenance
+headache. See also https://github.com/biod/sambamba/issues/425
+
++ Removed CRAM support and htslib dependency
+
 ## ChangeLog v0.7.1 (20191128)
 
 + Fixed major segfault problem that got introduced after ldc 1.10, see https://github.com/biod/sambamba/issues/393

VERSION

@@ -1 +1 @@
-0.7.1
+0.8.0