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--- a/Makefile
+++ b/Makefile
@@ -4,46 +4,29 @@
# (c) 2009 Aaron Quinlan
# ==========================
-SHELL := /bin/bash -e
+SHELL := bash -e
VERSION_FILE=./src/utils/version/version_git.h
RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
# define our object and binary directories
-ifeq ($(VERBOSE),1)
CCPREFIX =
-else
-CCPREFIX = @
-endif
OBJ_DIR = obj
BIN_DIR = bin
SRC_DIR = src
-CXX = g++
-
-PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3)
-
-ifeq ($(DEBUG),1)
-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
-else
BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
-BT_CXXFLAGS = -g -Wall -O2
-endif
+BT_CXXFLAGS = -Wall
# If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
-ifeq ($(USE_RAND),1)
-BT_CXXFLAGS += -DUSE_RAND
-else
BT_CXXFLAGS += -std=c++11
-endif
BT_LDFLAGS =
BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
-prefix ?= /usr/local
+prefix = $(EPREFIX)/usr
SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/bamToBed \
@@ -213,7 +196,7 @@
# make the "obj/" and "bin/" directories, if they don't exist
$(OBJ_DIR) $(BIN_DIR):
- @mkdir -p $@
+ mkdir -p $@
# Usually HTSlib's configure script has not been used (detected via config.mk
--- a/src/utils/htslib/Makefile
+++ b/src/utils/htslib/Makefile
@@ -22,20 +22,13 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
-CC = gcc
-AR = ar
-RANLIB = ranlib
-
# Default libraries to link if configure is not used
htslib_default_libs = -lz -lm -lbz2 -llzma
-CPPFLAGS =
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
-CFLAGS = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS =
LIBS = $(htslib_default_libs)
prefix = /usr/local
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