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83 lines
2.0 KiB
83 lines
2.0 KiB
--- a/Makefile
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+++ b/Makefile
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@@ -4,44 +4,29 @@
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# (c) 2009 Aaron Quinlan
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# ==========================
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-SHELL := /bin/bash -e
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+SHELL := bash -e
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VERSION_FILE=./src/utils/version/version_git.h
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RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
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# define our object and binary directories
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-ifeq ($(VERBOSE),1)
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CCPREFIX =
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-else
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-CCPREFIX = @
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-endif
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OBJ_DIR = obj
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BIN_DIR = bin
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SRC_DIR = src
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-CXX = g++
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-
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-ifeq ($(DEBUG),1)
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-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
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-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
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-else
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BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
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-BT_CXXFLAGS = -g -Wall -O2
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-endif
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+BT_CXXFLAGS = -Wall
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# If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
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-ifeq ($(USE_RAND),1)
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-BT_CXXFLAGS += -DUSE_RAND
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-else
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BT_CXXFLAGS += -std=c++11
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-endif
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BT_LDFLAGS =
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BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
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-prefix ?= /usr/local
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+prefix = $(EPREFIX)/usr
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SUBDIRS = $(SRC_DIR)/annotateBed \
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$(SRC_DIR)/bamToBed \
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@@ -204,7 +189,7 @@
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# make the "obj/" and "bin/" directories, if they don't exist
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$(OBJ_DIR) $(BIN_DIR):
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- @mkdir -p $@
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+ mkdir -p $@
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# Usually HTSlib's configure script has not been used (detected via config.mk
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--- a/src/utils/htslib/Makefile
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+++ b/src/utils/htslib/Makefile
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@@ -22,20 +22,13 @@
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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-CC = gcc
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-AR = ar
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-RANLIB = ranlib
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-
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# Default libraries to link if configure is not used
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htslib_default_libs = -lz -lm -lbz2 -llzma
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-CPPFLAGS =
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# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
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# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
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#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
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-CFLAGS = -g -Wall -O2
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EXTRA_CFLAGS_PIC = -fpic
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-LDFLAGS =
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LIBS = $(htslib_default_libs)
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prefix = /usr/local
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