Allow for unbundling htslib

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

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;
 

source/Makefile

@@ -12,12 +12,26 @@ CXXFLAGSextra ?=
 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_shared :=
+LDFLAGS_static := -static -static-libgcc
+LDFLAGS_Mac :=
+LDFLAGS_Mac_static := -static-libgcc
 LDFLAGS_gdb := $(LDFLAGS_shared)
 
+ifdef SYSTEM_HTSLIB
+PKG_CONFIG ?= pkg-config
+HTSLIB_CFLAGS = $(shell $(PKG_CONFIG) --cflags htslib)
+HTSLIB_LIBS = $(shell $(PKG_CONFIG) --libs htslib)
+else
+HTSLIB_DEP := htslib
+
+HTSLIB_CFLAGS := -Ihtslib/
+HTSLIB_LIBS := htslib/libhts.a -lz
+endif
+
+CPPFLAGS += $(HTSLIB_CFLAGS)
+LIBS += -pthread $(HTSLIB_LIBS)
+
 DATE_FMT = --iso-8601=seconds
 ifdef SOURCE_DATE_EPOCH
     BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)")
@@ -53,7 +67,7 @@ CXXFLAGS_gdb := -O0 -g3 $(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 \
 	SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o \
 	SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o \
-	Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp \
+	Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.o \
 	SoloFeature_cellFiltering.o \
 	SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o \
 	ParametersSolo.o SoloRead.o SoloRead_record.o \
@@ -74,22 +88,22 @@ OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMapper
 	ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o \
 	OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o \
 	ReadAlign_maxMappableLength2strands.o binarySearch2.o\
-	ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp \
+	ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.o \
 	ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o \
 	ReadAlign_stitchWindowSeeds.o \
 	ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o \
 	ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o\
 	ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o \
 	stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o \
-	ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o \
+	ChimericSegment.o ChimericAlign.o ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o \
 	Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o \
 	Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o \
 	TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o \
 	Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o \
 	ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o \
 	sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o \
-	Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o \
-	bam_cat.o serviceFuns.o GlobalVariables.cpp \
+	Parameters_readFilesInit.o Parameters_openReadsFiles.o Parameters_closeReadsFiles.o Parameters_readSAMheader.o \
+	bam_cat.o serviceFuns.o GlobalVariables.o \
 	BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o
 
 SOURCES := $(wildcard *.cpp) $(wildcard *.c)
@@ -130,7 +144,7 @@ ifneq ($(MAKECMDGOALS),CLEAN)
 ifneq ($(MAKECMDGOALS),clean_solo)
 ifneq ($(MAKECMDGOALS),STARforMac)
 ifneq ($(MAKECMDGOALS),STARforMacGDB)
-Depend.list: $(SOURCES) parametersDefault.xxd htslib
+Depend.list: $(SOURCES) parametersDefault.xxd $(HTSLIB_DEP)
 	echo $(SOURCES)
 	'rm' -f ./Depend.list
 	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
@@ -153,46 +167,46 @@ parametersDefault.xxd: parametersDefault
 STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
 STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
 STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR$(SFX) $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR$(SFX) $(OBJECTS) $(LIBS)
 
 STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
 STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
 STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR$(SFX) $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR$(SFX) $(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) $(CXXFLAGS) $(LDFLAGS) -o STARlong$(SFX) $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STARlong$(SFX) $(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) $(CXXFLAGS) $(LDFLAGS) -o STARlong$(SFX) $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STARlong$(SFX) $(OBJECTS) $(LIBS)
 
 
 
 POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
 POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
 POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR$(SFX) $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR$(SFX) $(OBJECTS) $(LIBS)
 
 gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
 gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
 gdb : Depend.list parametersDefault.xxd $(OBJECTS)
-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR $(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) $(CXXFLAGS) $(LDFLAGS) -o STARlong $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STARlong $(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) $(CXXFLAGS) $(LDFLAGS) -o STAR $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STAR $(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) $(CXXFLAGS) $(LDFLAGS) -o STARlong $(OBJECTS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS)

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) {

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"

source/bam_cat.c

@@ -52,8 +52,8 @@ THE SOFTWARE.
 #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

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);
 

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"