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--- a/source/bam_cat.c
+++ b/source/bam_cat.c
@@ -52,8 +52,8 @@
#include <stdlib.h>
#include <unistd.h>
-#include "htslib/htslib/bgzf.h"
-#include "htslib/htslib/sam.h"
+#include <htslib/bgzf.h>
+#include <htslib/sam.h>
#include <cstring>
#define BUF_SIZE 0x10000
--- a/source/bam_cat.h
+++ b/source/bam_cat.h
@@ -1,7 +1,7 @@
#ifndef CODE_bam_cat
#define CODE_bam_cat
-#include "htslib/htslib/sam.h"
+#include <htslib/sam.h>
int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
--- a/source/BAMfunctions.cpp
+++ b/source/BAMfunctions.cpp
@@ -1,5 +1,5 @@
#include "BAMfunctions.h"
-#include "htslib/htslib/kstring.h"
+#include <htslib/kstring.h>
string bam_cigarString (bam1_t *b) {//output CIGAR string
--- a/source/bamRemoveDuplicates.cpp
+++ b/source/bamRemoveDuplicates.cpp
@@ -1,7 +1,7 @@
#include <unordered_map>
#include "bamRemoveDuplicates.h"
#include <iostream>
-#include "htslib/htslib/sam.h"
+#include <htslib/sam.h>
#include "IncludeDefine.h"
#include SAMTOOLS_BGZF_H
#include "ErrorWarning.h"
--- a/source/IncludeDefine.h
+++ b/source/IncludeDefine.h
@@ -30,8 +30,8 @@
#define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
//external libs
-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
-#define SAMTOOLS_SAM_H "htslib/htslib/sam.h"
+#define SAMTOOLS_BGZF_H <htslib/bgzf.h>
+#define SAMTOOLS_SAM_H <htslib/sam.h>
using namespace std;
--- a/source/Makefile
+++ b/source/Makefile
@@ -12,11 +12,7 @@
CXX ?= g++
# pre-defined flags
-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
-LDFLAGS_gdb := $(LDFLAGS_shared)
+LIBS := -pthread -lhts -lz
DATE_FMT = --iso-8601=seconds
ifdef SOURCE_DATE_EPOCH
@@ -27,7 +23,7 @@
BUILD_PLACE ?= $(HOSTNAME):$(shell pwd)
-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"'
+COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""'
GIT_CHECK := $(shell git status 1> /dev/null 2> /dev/null && echo 0)
@@ -41,13 +37,13 @@
# Defaults, can be overridden by make arguments or environment
CXXFLAGS ?= -pipe -Wall -Wextra
-CFLAGS ?= -pipe -Wall -Wextra -O3
+CFLAGS ?= -pipe -Wall -Wextra
CXXFLAGS_SIMD ?= -mavx2
# Unconditionally set essential flags and optimization options
CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF)
-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
-CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
+CXXFLAGS_main := $(CXXFLAGS_common)
+CXXFLAGS_gdb := $(CXXFLAGS_common)
##########################################################################################################
OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o \
@@ -130,7 +126,7 @@
ifneq ($(MAKECMDGOALS),clean_solo)
ifneq ($(MAKECMDGOALS),STARforMac)
ifneq ($(MAKECMDGOALS),STARforMacGDB)
-Depend.list: $(SOURCES) parametersDefault.xxd htslib
+Depend.list: $(SOURCES) parametersDefault.xxd
echo $(SOURCES)
'rm' -f ./Depend.list
$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
@@ -142,57 +138,43 @@
endif
endif
-htslib : htslib/libhts.a
-
-htslib/libhts.a :
- $(MAKE) -C htslib lib-static
-
parametersDefault.xxd: parametersDefault
xxd -i parametersDefault > parametersDefault.xxd
STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
-STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
-STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
STARlong$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
-STARlong$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
STARlong$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
STARlongStatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
-STARlongStatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
STARlongStatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
-gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
gdb : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
-gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
-STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
-STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
+ $(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
--- a/source/signalFromBAM.h
+++ b/source/signalFromBAM.h
@@ -1,6 +1,6 @@
#ifndef CODE_signalFromBAM
#define CODE_signalFromBAM
-#include "htslib/htslib/sam.h"
+#include <htslib/sam.h>
#include <fstream>
#include <string>
#include "Stats.h"
--- a/source/STAR.cpp
+++ b/source/STAR.cpp
@@ -29,7 +29,7 @@
#include "twoPassRunPass1.h"
-#include "htslib/htslib/sam.h"
+#include <htslib/sam.h>
#include "parametersDefault.xxd"
void usage(int usageType) {
|
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