Commit 4fd8c8fc authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

New upstream version 1.2+dfsg

parent f241cdb3

Makefile

+63 −14
Original line number Diff line number Diff line
@@ -12,12 +12,12 @@ HTSLD_LIB= 
CXX=g++ -std=c++0x



#COMPILER FLAGS

CXXFLAG_REL=-O2

CXXFLAG_REL=-O3

CXXFLAG_DBG=-g

CXXFLAG_WRN=-Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter



#BASE LIBRARIES

LIB_FLAGS=-Wl,-Bstatic -lz -lgsl -lblas -lbz2 -Wl,-Bdynamic -lm -lpthread 

LIB_FLAGS=-lz -lgsl -lblas -lbz2 -llzma -lgslcblas -lm -lpthread



#FILE LISTS

BFILE=bin/QTLtools
@@ -27,16 +27,35 @@ CFILE=$(shell find src -name *.cpp) 
OFILE=$(shell for file in `find src -name *.cpp`; do echo obj/$$(basename $$file .cpp).o; done)

VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)



#DEFAULT VERSION (I.E. UNIGE DESKTOP RELEASE VERSION)

all: desktop

#DEFAULT VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)

all: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN)

all: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)

all: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a

all: LDFLAG=$(CXXFLAG_REL)

all: $(BFILE)



#DEFAULT DEBUG VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)

all-dbg: CXXFLAG=$(CXXFLAG_DBG) $(CXXFLAG_WRN)

all-dbg: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)

all-dbg: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a

all-dbg: LDFLAG=$(CXXFLAG_DBG)

all-dbg: $(BFILE)



#DEFAULT VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)

all-static: LIB_FLAGS=-Wl,-Bstatic -lz -lgsl -lblas -lbz2 -llzma -lgslcblas -Wl,-Bdynamic -lm -lpthread 

all-static: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN)

all-static: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)

all-static: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a

all-static: LDFLAG=$(CXXFLAG_REL)

all-static: $(BFILE)



#UNIGE DESKTOP RELEASE VERSION

desktop: RMATH_INC=$(HOME)/Tools/R-3.2.2/src/include

desktop: RMATH_LIB=$(HOME)/Tools/R-3.2.2/src/nmath/standalone

desktop: HTSLD_INC=$(HOME)/Tools/htslib-1.3.1

desktop: HTSLD_LIB=$(HOME)/Tools/htslib-1.3.1

desktop: HTSLD_INC=$(HOME)/Tools/htslib-1.3

desktop: HTSLD_LIB=$(HOME)/Tools/htslib-1.3

desktop: BOOST_INC=/usr/include

desktop: BOOST_LIB=/usr/lib

desktop: BOOST_LIB=/usr/lib/x86_64-linux-gnu

desktop: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN)

desktop: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)

desktop: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a
@@ -44,15 +63,24 @@ desktop: LDFLAG=$(CXXFLAG_REL) 
desktop: $(BFILE)



#UNIGE DESKTOP DEBUG VERSION

desktop-dbg: desktop

desktop-dbg: RMATH_INC=$(HOME)/Tools/R-3.2.2/src/include

desktop-dbg: RMATH_LIB=$(HOME)/Tools/R-3.2.2/src/nmath/standalone

desktop-dbg: HTSLD_INC=$(HOME)/Tools/htslib-1.3

desktop-dbg: HTSLD_LIB=$(HOME)/Tools/htslib-1.3

desktop-dbg: BOOST_INC=/usr/include

desktop-dbg: BOOST_LIB=/usr/lib/x86_64-linux-gnu

desktop-dbg: CXXFLAG=$(CXXFLAG_DBG) $(CXXFLAG_WRN)

desktop-dbg: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)

desktop-dbg: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a

desktop-dbg: LDFLAG=$(CXXFLAG_DBG)

desktop-dbg: $(BFILE)



#VITAL-IT RELEASE VERSION

cluster: RMATH_INC=/software/R/3.1.1/include

cluster: RMATH_LIB=/software/R/3.1.1/lib64

cluster: HTSLD_INC=/software/UHTS/Analysis/samtools/1.2/include

cluster: HTSLD_LIB=/software/UHTS/Analysis/samtools/1.2/lib64

cluster: LIB_FLAGS=-lz -lgsl -lblas -lbz2 -lm -lpthread -lgslcblas -llzma

cluster: RMATH_INC=/software/R/3.4.2/include

cluster: RMATH_LIB=/software/R/3.4.2/lib64

cluster: HTSLD_INC=/software/UHTS/Analysis/samtools/1.4/include

cluster: HTSLD_LIB=/software/UHTS/Analysis/samtools/1.4/lib64

cluster: BOOST_INC=/software/include

cluster: BOOST_LIB=/software/lib64

cluster: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN)
@@ -62,9 +90,18 @@ cluster: LDFLAG=$(CXXFLAG_REL) 
cluster: $(BFILE)



#VITAL-IT DEBUG VERSION

cluster-dbg: cluster

cluster-dbg: LIB_FLAGS=-lz -lgsl -lblas -lbz2 -lm -lpthread -lgslcblas -llzma

cluster-dbg: RMATH_INC=/software/R/3.4.2/include

cluster-dbg: RMATH_LIB=/software/R/3.4.2/lib64

cluster-dbg: HTSLD_INC=/software/UHTS/Analysis/samtools/1.4/include

cluster-dbg: HTSLD_LIB=/software/UHTS/Analysis/samtools/1.4/lib64

cluster-dbg: BOOST_INC=/software/include

cluster-dbg: BOOST_LIB=/software/lib64

cluster-dbg: CXXFLAG=$(CXXFLAG_DBG) $(CXXFLAG_WRN)

cluster-dbg: LDFLAG=$(CXXFLAG_DBG)

cluster-dbg: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)

cluster-dbg: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a

cluster-dbg: $(BFILE)



#MAC RELEASE VERSION

mac: RMATH_INC=$(HOME)/Libraries/R-3.2.2/src/include
@@ -132,7 +169,7 @@ obj/union_%.o: union_%.cpp union_data.h src/common/data.h src/common/filter.h $( 
obj/extract_%.o: extract_%.cpp extract_data.h src/common/data.h src/common/filter.h $(TFILE)

	$(CXX) -o $@ -c $< $(CXXFLAG) $(IFLAG)



obj/quan_%.o: quan_%.cpp quan_data.h src/common/data.h src/common/filter.h $(TFILE)

obj/quan_%.o: quan_%.cpp quan_data.h quan_xxhash.h src/common/data.h src/common/filter.h $(TFILE)

	$(CXX) -o $@ -c $< $(CXXFLAG) $(IFLAG)

	

obj/ase_%.o: ase_%.cpp ase_data.h src/common/data.h src/common/filter.h $(TFILE)
@@ -144,6 +181,12 @@ obj/bamstat_%.o: bamstat_%.cpp bamstat_data.h src/common/data.h src/common/filte 
obj/fdensity_%.o: fdensity_%.cpp fdensity_data.h src/common/data.h src/common/filter.h $(TFILE)

	$(CXX) -o $@ -c $< $(CXXFLAG) $(IFLAG)

	

obj/rep_%.o: rep_%.cpp rep_data.h src/common/data.h src/common/filter.h $(TFILE)

	$(CXX) -o $@ -c $< $(CXXFLAG) $(IFLAG)

	

obj/gwas_%.o: gwas_%.cpp gwas_data.h src/common/data.h src/common/filter.h $(TFILE)

	$(CXX) -o $@ -c $< $(CXXFLAG) $(IFLAG)

	

clean: 

	rm -f obj/*.o $(BFILE)
@@ -189,4 +232,10 @@ clean-bamstat: 
clean-fdensity:

	rm -f obj/fdensity_*.o $(BFILE)

		

clean-rep:

	rm -f obj/rep_*.o $(BFILE)

		

clean-gwas:

	rm -f obj/gwas_*.o $(BFILE)

		

		
 No newline at end of file

lib/OTools/residualizer.h

+3 −3
Original line number Diff line number Diff line
@@ -77,7 +77,7 @@ public: 
		for (set < unsigned int >::iterator itNM = i_nonmissing.begin(); itNM != i_nonmissing.end() ; ++itNM) {

			float value;

			std::istringstream in(covariate[*itNM]);

			if (!(in >> value)) {

			if (!(in >> value) || in.rdbuf()->in_avail() != 0) {

				factors.insert(covariate[*itNM]);

				isAlphabetic = true;

			} else isNumeric = true;
@@ -88,12 +88,12 @@ public: 
		vector < vector < float > > additional_hcov;

		if (factors.size() == 0) {

			additional_hcov = vector < vector < float > > (1, vector < float > (n_samples, 0.0));

			for (int i = 0 ; i < covariate.size() ; i++) additional_hcov[0][i] = std::stof(covariate[i]);

			for (int i = 0 ; i < covariate.size() ; i++) if (i_nonmissing.count(i)) additional_hcov[0][i] = std::stof(covariate[i]);

		} else if (factors.size() > 1) {

			factors.erase(factors.begin());

			for (set < string > ::iterator itF = factors.begin(); itF != factors.end() ; itF++) {

				additional_hcov.push_back(vector < float > (n_samples, 0.0));

				for (int i = 0 ; i < n_samples ; i++) additional_hcov.back()[i] = (covariate[i] == (*itF));

				for (int i = 0 ; i < n_samples ; i++) if (i_nonmissing.count(i)) additional_hcov.back()[i] = (covariate[i] == (*itF));

			}

		} else return COV_DROP;

lib/OTools/string_utils.h

+1 −1
Original line number Diff line number Diff line
@@ -49,7 +49,7 @@ public: 
		float n;

		std::istringstream in(str);

		if (!(in >> n)) return false;

		return true;

		return in.rdbuf()->in_avail() == 0;

	}



	template < class T >

src/QTLtools.cpp

+14 −4
Original line number Diff line number Diff line
@@ -27,6 +27,8 @@ 
#include "mode_union/union_data.h"

#include "mode_bamstat/bamstat_data.h"

#include "mode_fdensity/fdensity_data.h"

#include "mode_rep/rep_data.h"

#include "mode_gwas/gwas_data.h"



void printModes(){

    vrb.ctitle("Usage:");
@@ -47,6 +49,8 @@ void printModes(){ 
    vrb.print("  extract   Data extraction mode");

    vrb.print("  quan      Quantification mode");

    vrb.print("  ase       Measure allelic imbalance at every het genotype");

    vrb.print("  rep       Replicate QTL associations into independent data set");

    vrb.print("  gwas      GWAS tests");

}



int main(int argc, char ** argv) {
@@ -69,7 +73,7 @@ int main(int argc, char ** argv) { 
	vrb.bullet("Webpage : https://qtltools.github.io/qtltools/");

	vrb.bullet("Version : " + string(QTLTOOLS_VERSION));

	vrb.bullet("Date    : " + running_timer.date());

	if (!match_mode) vrb.bullet("Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1101/068635");

	if (!match_mode) vrb.bullet("Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452");

	else vrb.bullet("Citation: MBV; a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay data sets");



	//4. Switch mode
@@ -111,7 +115,7 @@ int main(int argc, char ** argv) { 
    else if (strcmp(argv[1], "rtc-union") == 0) union_main(args);



    //5.11. QUANTIFICATION mode

    else if (strcmp(argv[1], "quan") == 0) quan_main(args);

    else if (strcmp(argv[1], "quan") == 0) quan2_main(args);



    //5.12. ASE mode

    else if (strcmp(argv[1], "ase") == 0) ase_main(args);
@@ -122,7 +126,13 @@ int main(int argc, char ** argv) { 
    //5.14. FDENSITY mode

    else if (strcmp(argv[1], "fdensity") == 0) fdensity_main(args);



	//5.15. UNRECOGNIZED mode

    //5.15. REPLICATION mode

    else if (strcmp(argv[1], "rep") == 0) rep_main(args);



    //5.16. GWAS mode

    else if (strcmp(argv[1], "gwas") == 0) gwas_main(args);



	//5.17. UNRECOGNIZED mode

    else if (strcmp(argv[1], "--help") == 0) {

        printModes();

        exit(EXIT_SUCCESS);

src/common/data.h

+1 −1
Original line number Diff line number Diff line
@@ -19,7 +19,7 @@ 
#include "otools.h"

#include "filter.h"



#define QTLTOOLS_VERSION "1.1"

#define QTLTOOLS_VERSION "1.2"



class data {

public: