1 files changed, 0 insertions, 87 deletions
diff --git a/makefile-system-htslib.patch b/makefile-system-htslib.patch
deleted file mode 100644
index 7e98ae5d9f98..000000000000
--- a/makefile-system-htslib.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- Makefile.orig	2017-03-14 07:26:49.191430557 +0100
-+++ Makefile	2017-03-14 07:27:44.929678345 +0100
-@@ -29,20 +29,10 @@
- all: $(PROG) $(TEST_PROG)
- 
- # Adjust $(HTSDIR) to point to your top-level htslib directory
--HTSDIR = htslib-1.4.1
--include $(HTSDIR)/htslib.mk
--include $(HTSDIR)/htslib_static.mk
--HTSLIB = $(HTSDIR)/libhts.a
--BGZIP  = $(HTSDIR)/bgzip
--TABIX  = $(HTSDIR)/tabix
--HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
--HTSLIB_LIBS = $(HTSLIB_static_LIBS)
-+HTSDIR = /usr/include
- 
- CC       = gcc
--CPPFLAGS =
--CFLAGS   = -g -Wall -Wc++-compat -O2
--LDFLAGS  =
--LIBS     =
-+CFLAGS   := -g -Wall -Wc++-compat -O2 $(CFLAGS)
- 
- ifeq "$(shell uname -s)" "Darwin"
- DYNAMIC_FLAGS = -Wl,-export_dynamic
-@@ -51,8 +41,8 @@
- endif
- 
- # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
--ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
--ALL_LDFLAGS  = $(DYNAMIC_FLAGS) $(HTSLIB_LDFLAGS) $(LDFLAGS)
-+ALL_CPPFLAGS = -I. $(CPPFLAGS)
-+ALL_LDFLAGS  = $(DYNAMIC_FLAGS) $(LDFLAGS)
- ALL_LIBS     = -lm -lz -ldl $(LIBS)
- 
- OBJS     = main.o vcfindex.o tabix.o \
-@@ -64,7 +54,7 @@
-            mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
-            ccall.o em.o prob1.o kmin.o # the original samtools calling
- 
--EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
-+EXTRA_CPPFLAGS = -I. -DPLUGINPATH=\"$(pluginpath)\"
- GSL_LIBS       =
- 
- # The polysomy command is not compiled by default because it brings dependency
-@@ -73,7 +63,7 @@
- ifdef USE_GPL
-     EXTRA_CPPFLAGS += -DUSE_GPL
-     OBJS += polysomy.o peakfit.o
--    GSL_LIBS = -lgsl -lcblas
-+    GSL_LIBS = -lgsl -lgslcblas
- endif
- 
- prefix      = /usr/local
-@@ -117,12 +107,12 @@
- .c.o:
- 	$(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
- 
--test: $(PROG) plugins test/test-rbuf test/test-regidx $(BGZIP) $(TABIX)
-+test: $(PROG) plugins test/test-rbuf test/test-regidx
- 	./test/test-regidx
--	./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
-+	./test/test.pl --exec bgzip=bgzip --exec tabix=tabix
- 
--test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
--	./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
-+test-plugins: $(PROG) plugins test/test-rbuf
-+	./test/test.pl --plugins --exec bgzip=bgzip --exec tabix=tabix
- 
- 
- # Plugin rules
-@@ -208,11 +198,11 @@
- 
- test/test-regidx.o: test/test-regidx.c regidx.h
- 
--test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS)
-+test/test-regidx: test/test-regidx.o regidx.o
-+	$(CC) $(ALL_LDFLAGS) -o $@ $^ -lpthread -lhts $(ALL_LIBS)
- 
--bcftools: $(HTSLIB) $(OBJS)
--	$(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
-+bcftools: $(OBJS)
-+	$(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) -lpthread -lhts $(GSL_LIBS) $(ALL_LIBS)
- 
- doc/bcftools.1: doc/bcftools.txt
- 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt