<commit_before>
CC = gcc

WRAP_MALLOC = -DUSE_MALLOC_WRAPPERS
CFLAGS = -g -Wall -O2 -Wno-unused-function -std=c99
DFLAGS = -DHAVE_PTHREAD $(WRAP_MALLOC)
LIBS = -lm -lz -lpthread
INCLUDES= aligner.h

SOURCES = rapi_bwa.c rapi.c bwamem.c
OBJS = $(SOURCES:.c=.o)

.SUFFIXES:.c .o

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) $< -o $@

all: rapi

rapi: libbwa.a $(OBJS)
	$(CC) $(CFLAGS) $(OBJS) -o rapi -L. -lbwa $(LIBS) 

clean:
	rm -f $(OBJS)<commit_msg>Build with BWA is user-specified path<commit_after>

CC = gcc

WRAP_MALLOC = -DUSE_MALLOC_WRAPPERS
CFLAGS = -g -Wall -O2 -Wno-unused-function -std=c99
DFLAGS = -DHAVE_PTHREAD $(WRAP_MALLOC)
LIBS = -lm -lz -lpthread

# these depend on BWA_PATH
INCLUDES := -I../../ -I$(BWA_PATH)
SOURCES := rapi_bwa.c rapi.c $(BWA_PATH)/bwamem.c
# we define the object names from the source names, substituting the
# extension and keeping online the file name (removing the directory part)
OBJS := $(notdir $(SOURCES:.c=.o))

.SUFFIXES:.c .o

.PHONY: bwa clean

.c.o:
	$(CC) -c $(CFLAGS) $(INCLUDES) $(DFLAGS) $< -o $@

all: rapi

rapi: bwa $(BWA_PATH)/libbwa.a $(OBJS)
	$(CC) $(CFLAGS) $(OBJS) -o rapi -L$(BWA_PATH) -lbwa $(LIBS) 

bwa:
	@echo "BWA_PATH is $(BWA_PATH)"
	$(if $(BWA_PATH),, $(error "You need to set the BWA_PATH variable on the cmd line to point to the compiled BWA source code (e.g., make BWA_PATH=/tmp/bwa)"))

bwamem.o: bwa $(BWA_PATH)/bwamem.c
	$(CC) -c $(CFLAGS) $(INCLUDES) $(DFLAGS) $(BWA_PATH)/bwamem.c -o $@

clean:
	rm -f $(OBJS)
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{'dir': 'git-commits-cleaned', 'id': '7621374', 'n_tokens_mistral': 704, 'n_tokens_neox': 666, 'n_words': 179}