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Merge pull request #1 from lh3/new-mak

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New makefile; fixed a compiling error
This commit is contained in:
chhylp123
2019-11-22 15:13:20 -05:00
committed by GitHub
parent c7419d3e5e db7e31f90d
commit 2a8e0dc254
3 changed files with 60 additions and 15 deletions
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Makefile
+48 -12
View File
@@ -1,18 +1,54 @@
CC=g++
CXX= g++
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Winline -Wall
CPPFLAGS=
INCLUDES=
OBJS= Output.o CommandLines.o Process_Read.o Assembly.o kmer.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o edlib.o Overlaps.o
EXE= ccs_assembly
LIBS= -lz -lpthread -lm
CFLAGS = -w -c -msse4.2 -mpopcnt -fomit-frame-pointer -Winline -O3 -lz
LDFLAGS = -lm -lz -lpthread -O3 -mpopcnt -msse4.2 -lz -w
ifneq ($(asan),)
CXXFLAGS+=-fsanitize=address
LIBS+=-fsanitize=address
endif
SOURCES = main.cpp Output.cpp CommandLines.cpp Process_Read.cpp Assembly.cpp kmer.cpp Hash_Table.cpp POA.cpp Correct.cpp Levenshtein_distance.cpp edlib.cpp Overlaps.cpp
OBJECTS = $(SOURCES:.c=.o)
EXECUTABLE = ccs_assembly
.SUFFIXES:.cpp .o
.PHONY:all clean depend
.cpp.o:
$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
all: $(SOURCES) $(EXECUTABLE)
$(EXECUTABLE): $(OBJECTS)
$(CC) $(OBJECTS) -o $@ $(LDFLAGS)
all:$(EXE)
$(EXE):$(OBJS) main.o
$(CXX) $(CXXFLAGS) $^ -o $@ $(LIBS)
.c.o:
$(CC) $(CFLAGS) $< -o $@
clean:
rm -f *.o *~ \#* ccs_assembly
rm -fr gmon.out *.o a.out $(EXE) *~ *.a *.dSYM
depend:
(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CPPFLAGS) $(DFLAGS) -- *.cpp)
# DO NOT DELETE
Assembly.o: Assembly.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
Assembly.o: CommandLines.h kmer.h Hash_Table.h khash.h POA.h Correct.h
Assembly.o: Levenshtein_distance.h Output.h
CommandLines.o: CommandLines.h ketopt.h
Correct.o: Correct.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h
Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h Levenshtein_distance.h
Correct.o: POA.h edlib.h Assembly.h
Hash_Table.o: Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h
Hash_Table.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
Hash_Table.o: POA.h ksort.h
Levenshtein_distance.o: Levenshtein_distance.h
Output.o: Output.h CommandLines.h
Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h kseq.h
Overlaps.o: CommandLines.h
POA.o: POA.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h
POA.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
edlib.o: edlib.h
kmer.o: kmer.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
main.o: Assembly.h Levenshtein_distance.h edlib.h
Overlaps.cpp
+2 -1
View File
@@ -1,5 +1,6 @@
#include <stdio.h>
#include <stdlib.h>
#define __STDC_LIMIT_MACROS
#include <stdint.h>
#include "Overlaps.h"
#include "ksort.h"
@@ -8404,4 +8405,4 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
asg_destroy(sg);
free(coverage_cut);
}
}
kseq.h
+10 -2
View File
@@ -37,6 +37,14 @@
#define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
#define KS_SEP_MAX 2
#ifndef klib_unused
#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
#define klib_unused __attribute__ ((__unused__))
#else
#define klib_unused
#endif
#endif /* klib_unused */
#define __KS_TYPE(type_t) \
typedef struct __kstream_t { \
unsigned char *buf; \
@@ -65,7 +73,7 @@
}
#define __KS_GETC(__read, __bufsize) \
static inline int ks_getc(kstream_t *ks) \
static inline klib_unused int ks_getc(kstream_t *ks) \
{ \
if (ks_err(ks)) return -3; \
if (ks->is_eof && ks->begin >= ks->end) return -1; \
@@ -231,7 +239,7 @@ typedef struct __kstring_t {
__KSEQ_BASIC(SCOPE, type_t) \
__KSEQ_READ(SCOPE)
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static klib_unused, type_t, __read)
#define KSEQ_DECLARE(type_t) \
__KS_TYPE(type_t) \