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SMR.cpp
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//
// SMR.cpp
// SRM_CPP
//
// Created by Futao Zhang on 29/06/15.
// Copyright (c) 2015 Futao Zhang. All rights reserved.
//
#include "StrFunc.h"
#include "SMR_data_p1.h"
#include "SMR_data_p2.h"
#include "SMR_data_p3.h"
#include "SMR_data_p4.h"
#include "SMR_plot.h"
#include "bfile.hpp"
#include "SMR.h"
using namespace SMRDATA;
using namespace StatFunc;
int thread_num;
bool mute = false;
int xh=0;
bool forcefrqck = true;
char* outFileName=NULL;
int main(int argc, char** argv) {
cout << "*******************************************************************" << endl;
cout << "* SMR-IVW: Extension of Summary-data-based Mendelian Randomization (SMR)" << endl;
cout << "* version 1.0"<< endl;
cout << "* (C) 2015 Futao Zhang, Zhihong Zhu and Jian Yang" << endl;
cout << "* The University of Queensland" << endl;
cout << "* Extensions implemented by Marie Sadler, University of Lausanne"<< endl;
cout << "* MIT License" << endl;
cout << "*******************************************************************" << endl;
FLAGS_VALID_CK(argc,argv);
long int time_used = 0, start = time(NULL);
string months[] = {"Jan", "Feb", "Mar", "Apr", "May",
"Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"};
string weeks[] = {"Sun","Mon", "Tue", "Wed", "Thu", "Fri",
"Sat" };
time_t t = time(0);
tm* now = localtime(&t);
cout << "Analysis started: "<<now->tm_hour<<":"<<now->tm_min<<":"<< now->tm_sec<<","<<weeks[now->tm_wday]<<" "<<months[(now->tm_mon)]<<" "<<now->tm_mday<<","<<(now->tm_year + 1900)<<endl;
cout << "\nOptions:" << endl;
try {
option(argc, argv);
} catch (const string &err_msg) {
cerr << "\n" << err_msg << endl;
} catch (const char *err_msg) {
cerr << "\n" << err_msg << endl;
}
t = time(0);
now = localtime(&t);
cout << "\nAnalysis completed: "<<now->tm_hour<<":"<<now->tm_min<<":"<< now->tm_sec<<","<<weeks[now->tm_wday]<<" "<<months[(now->tm_mon)]<<" "<<now->tm_mday<<","<<(now->tm_year + 1900)<<endl;
time_used = time(NULL) - start;
cout << "Computational time: " << time_used / 3600 << ":" << (time_used % 3600) / 60 << ":" << time_used % 60 << endl;
return 0;
}
void option(int option_num, char* option_str[])
{
char* bFileName=NULL;
char* gwasFileName=NULL;
char* eqtlFileName=NULL;
char* indilstName=NULL;
char* snplstName=NULL;
char* indilst2remove=NULL;
char* snplst2exclde=NULL;
char* problst2exclde=NULL;
char* eproblst2exclde=NULL;
char* oproblst2exclde=NULL;
bool bFlag=false;// for binary file
double maf=0.0;
double p_hetero=1.5654e-3;
double p_smr=5.0e-8;
double p_medsmr=5.0e-8;
double p_gwas=5.0e-8;
double ld_prune=0.9;
double ld_min=0.05;
double ld_prune_multi=0.1;
unsigned int m_hetero=3;
int opt_hetero=20;
bool smr_flag=true;
bool smr_trans_flag=false;
// for data management
bool make_besd_flag=false;
char* problstName=NULL;
char* eproblstName=NULL;
char* oproblstName=NULL;
char* targetsnpproblstName=NULL;
char* snpproblstName=NULL;
char* eFileName=NULL;
bool eremlFlag=false;
double pexsnp = -9;
double pinsnp = -9;
// for filtering
bool cis_flag=false;
int cis_itvl=2000;
int trans_itvl=1000;
double transThres=5.0e-8;
double cisThres=5.0e-8;
double restThres=1.0e-5;
// for lookup
double plookup=5e-8;
bool lookup_flag=false;
char* genelistName=NULL;
int chr=0;
int prbchr=0;
int snpchr=0;
char* snprs=NULL;
char* snp2rm = NULL;
char* prbname=NULL;
char* fromsnprs=NULL;
char* tosnprs=NULL;
char* fromprbname=NULL;
char* toprbname=NULL;
int snpWind=50; //Kb
int prbWind=1000; //Kb
char* genename=NULL;
int fromsnpkb=-9;
int tosnpkb=-9;
int fromprbkb=-9;
int toprbkb=-9;
bool snpwindFlag=false;
bool prbwindFlag=false;
bool trans_dense=false;
char* refSNP=NULL;
bool heidioffFlag = false;
thread_num = 1;
bool combineFlg = false;
char* eqtlsmaslstName = NULL;
//
char* gwasFileName2=NULL;
char* eqtlFileName2=NULL; // for the outcome trait
char* traitlstName=NULL;
//
bool plotflg=false;
//
char* syllabusName=NULL;
bool gctaflag=false;
bool plinkflag=false;
bool gemmaflag=false;
bool merlinflag=false;
bool boltflag=false;
bool mateqtlflag = false;
bool fastqtlnflag = false;
bool fastqtlpflag = false;
bool qtltoolsnflag = false;
bool qtltoolspflag = false;
bool genouni=false;
char* freqName=NULL;
bool esdstd=false;
char* vpFileName=NULL;
bool metaflg=false;
bool est_effe_spl_size_flg=false;
// for SMR e2me
int outcomePrbWind=2000; //kb
char* eprobe=NULL;
char* oprobe=NULL;
char* eprobe2rm=NULL;
char* oprobe2rm=NULL;
bool prbmatch=false;
bool e2e_cis=false;
bool mediation=false;
bool mediation_multiple_cis=false;
bool mediation_multiple_trans=false;
// for MR-IVW Steiger filtering
double trev = -2;
// for mediation analysis
bool multi_corr_snp_flg = true;
bool get_snp_effects_flg = false;
bool get_snp_effects_top_flg = false;
int min_snp = 3;
char* core_med_lst = NULL;
char* qtl_med_lst = NULL;
char* med_corr_snps_lst = NULL;
bool incmp_expo = false;
int num_med = -9;
double med_R_thresh=-9;
bool uncorr_med = false;
bool exclude_top_SNP = false;
double p_shrinkage=1;
double p_expo_med = 0.01;
bool calcul_cormat_flag = false;
// for internal test
char* smrRltFileName = NULL;
bool recodeflg=false;
// for setBased SMR
char* geneAnnoName=NULL;
char* setlstName=NULL;
int setWind=-9;
bool ssmrflg=false;
bool ssmrivwflg=false;
bool ssmrivwtransflg=false;
bool ssmrrevflg=false;
bool ssmrgwastogwasflg=false;
bool ldmatrix=false;
//
char* queryFileName=NULL;
bool queryfileflg=false;
bool save_dense_flag=false;
double pthres_me2esmr=1.0;
double threshpsmrest=1.0;
double threshphet=0.0;
bool qcflag=false;
int qcmtd=0;
int z_thresh=3;
bool new_het_mth=true;
bool count_cis_flag = false;
bool count_trans_flag = false;
// for pick up instrument.// inflation, DO NOT USE
bool opt_slct_flag = false;
int meta_mtd = 0; //0 for meta, 1 for mecs
double pmecs = 0.01;
int nmecs = 100; // the number of common SNPs to calculation the correlation in MeCS
bool extract_cis_only = false;
bool rm_technical = false;
char* prbseqregion = NULL;
double ptech = 5.0e-8;
int addn=-9;
bool shownflag=false;
char* refepiName = NULL;
char* refesiName = NULL;
//for molecular trait
bool cis2all = false;
bool sampleoverlap = false;
int minsnpcor = 2;
double diff_freq = 0.2;
double diff_freq_ratio = 0.05;
int ldWind = 4000;
bool ldr = false;
bool ldr2 = false;
char* bldFileName = NULL;
bool make_bld_flag = false;
for(int i=0;i<option_num;i++)
{
// Plink files for LD from a reference sample
if(0==strcmp(option_str[i],"--bfile")){
bFileName=option_str[++i];
FLAG_VALID_CK("--bfile", bFileName);
printf("--bfile %s\n",bFileName);
}
else if(0==strcmp(option_str[i],"--bld")){
bldFileName=option_str[++i];
FLAG_VALID_CK("--bld", bldFileName);
printf("--bld %s\n",bldFileName);
}
else if(strcmp(option_str[i],"--make-bld")==0){
make_bld_flag=true;
cout<<"--make-bld "<<endl;
}
// gwas data file as cojo format
else if(0==strcmp(option_str[i],"--gwas-summary")){
if(gwasFileName ==NULL){
gwasFileName=option_str[++i];
FLAG_VALID_CK("--gwas-summary", gwasFileName);
printf("--gwas-summary %s\n",gwasFileName);
CommFunc::FileExist(gwasFileName);
}else
{
gwasFileName2=option_str[++i];
FLAG_VALID_CK("--gwas-summary", gwasFileName2);
printf("--gwas-summary %s\n",gwasFileName2);
CommFunc::FileExist(gwasFileName2);
}
}
// eQTL files
else if(0==strcmp(option_str[i],"--eqtl-summary")){
if(eqtlFileName==NULL)
{
eqtlFileName=option_str[++i];
FLAG_VALID_CK("--eqtl-summary", eqtlFileName);
printf("--eqtl-summary %s\n",eqtlFileName);
}else{
eqtlFileName2=option_str[++i];
FLAG_VALID_CK("--eqtl-summary", eqtlFileName2);
printf("--eqtl-summary %s\n",eqtlFileName2);
}
}
else if(0==strcmp(option_str[i],"--beqtl-summary")){
bFlag=true;
if(eqtlFileName==NULL)
{
eqtlFileName=option_str[++i];
FLAG_VALID_CK("--beqtl-summary", eqtlFileName);
printf("--beqtl-summary %s\n",eqtlFileName);
}else{
eqtlFileName2=option_str[++i];
FLAG_VALID_CK("--beqtl-summary", eqtlFileName2);
printf("--beqtl-summary %s\n",eqtlFileName2);
}
}
else if(strcmp(option_str[i],"--keep")==0){
indilstName=option_str[++i];
FLAG_VALID_CK("--keep", indilstName);
cout<<"--keep "<<indilstName<<endl;
CommFunc::FileExist(indilstName);
}
else if(strcmp(option_str[i],"--remove")==0){
indilst2remove=option_str[++i];
FLAG_VALID_CK("--remove", indilst2remove);
cout<<"--remove "<<indilst2remove<<endl;
CommFunc::FileExist(indilst2remove);
}
else if(strcmp(option_str[i],"--extract-snp")==0){
snplstName=option_str[++i];
FLAG_VALID_CK("--extract-snp", snplstName);
cout<<"--extract-snp "<<snplstName<<endl;
CommFunc::FileExist(snplstName);
}
else if(strcmp(option_str[i],"--extract-snp-p")==0){
pinsnp=atof(option_str[++i]);
cout<<"--extract-snp-p "<<pinsnp<<endl;
if(pinsnp<0 || pinsnp>1)
{
fprintf (stderr, "Error: --extract-snp-p should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--exclude-snp-p")==0){
pexsnp=atof(option_str[++i]);
cout<<"--exclude-snp-p "<<pexsnp<<endl;
if(pexsnp<0 || pexsnp>1)
{
fprintf (stderr, "Error: --exclude-snp-p should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--extract-probe")==0){
problstName=option_str[++i];
FLAG_VALID_CK("--extract-probe", problstName);
cout<<"--extract-probe "<<problstName<<endl;
CommFunc::FileExist(problstName);
}
else if(strcmp(option_str[i],"--extract-exposure-probe")==0){
eproblstName=option_str[++i];
FLAG_VALID_CK("--extract-exposure-probe", eproblstName);
cout<<"--extract-exposure-probe "<<eproblstName<<endl;
CommFunc::FileExist(eproblstName);
}
else if(strcmp(option_str[i],"--extract-outcome-probe")==0){
oproblstName=option_str[++i];
FLAG_VALID_CK("--extract-outcome-probe", oproblstName);
cout<<"--extract-outcome-probe "<<oproblstName<<endl;
CommFunc::FileExist(oproblstName);
}
else if(strcmp(option_str[i],"--exclude-snp")==0){
snplst2exclde=option_str[++i];
FLAG_VALID_CK("--exclude-snp", snplst2exclde);
cout<<"--exclude-snp "<<snplst2exclde<<endl;
CommFunc::FileExist(snplst2exclde);
}
else if(strcmp(option_str[i],"--exclude-probe")==0){
problst2exclde=option_str[++i];
FLAG_VALID_CK("--exclude-probe", problst2exclde);
cout<<"--exclude-probe "<<problst2exclde<<endl;
CommFunc::FileExist(problst2exclde);
}
else if(strcmp(option_str[i],"--exclude-exposure-probe")==0){
eproblst2exclde=option_str[++i];
FLAG_VALID_CK("--exclude-exposure-probe", eproblst2exclde);
cout<<"--exclude-exposure-probe "<<eproblst2exclde<<endl;
CommFunc::FileExist(eproblst2exclde);
}
else if(strcmp(option_str[i],"--exclude-outcome-probe")==0){
oproblst2exclde=option_str[++i];
FLAG_VALID_CK("--exclude-outcome-probe", oproblst2exclde);
cout<<"--exclude-outcome-probe "<<oproblst2exclde<<endl;
CommFunc::FileExist(oproblst2exclde);
}
else if(strcmp(option_str[i],"--maf")==0){
maf=atof(option_str[++i]);
cout<<"--maf "<<maf<<endl;
if(maf<0 || maf>0.5)
{
fprintf (stderr, "Error: --maf should be within the range from 0 to 0.5.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--make-besd")==0){
make_besd_flag=true;
cout<<"--make-besd "<<endl;
}
else if (0 == strcmp(option_str[i], "--out")){
outFileName = option_str[++i];
if(outFileName !=NULL && has_prefix(outFileName, "--"))
{
outFileName=NULL;
i--;
}else printf("--out %s\n", outFileName);
}
else if (0 == strcmp(option_str[i], "--peqtl-smr")){
p_smr = atof(option_str[++i]);
printf("--peqtl-smr %10.2e\n", p_smr);
if(p_smr<0 || p_smr>1)
{
fprintf (stderr, "Error: --peqtl-smr should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--pmqtl-smr")){
p_medsmr = atof(option_str[++i]);
printf("--pmqtl-smr %10.2e\n", p_medsmr);
if(p_medsmr<0 || p_medsmr>1)
{
fprintf (stderr, "Error: --pmqtl-smr should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--pgwas-smr")){
p_gwas = atof(option_str[++i]);
printf("--pgwas-smr %10.2e\n", p_gwas);
if(p_gwas<0 || p_gwas>1)
{
fprintf (stderr, "Error: --pgwas-smr should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--peqtl-heidi")){
p_hetero = atof(option_str[++i]);
printf("--peqtl-heidi %10.2e\n", p_hetero);
if(p_hetero<0 || p_hetero>1)
{
fprintf (stderr, "Error: --peqtl-heidi should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--heidi-min-m")){
m_hetero = atoi(option_str[++i]);
printf("--heidi-min-m %d\n", m_hetero);
}
else if (0 == strcmp(option_str[i], "--heidi-max-m")){
opt_hetero = atoi(option_str[++i]);
printf("--heidi-max-m %d\n", opt_hetero);
}
else if (0 == strcmp(option_str[i], "--heidi-mtd")){
int mtd=atoi(option_str[++i]);
if(mtd==0) new_het_mth=false;
else if(mtd==1) new_het_mth=true;
else {
printf("ERROR: only tow HEIDI methold avaliable.\n");
exit(EXIT_FAILURE);
}
printf("--heidi-mtd %d\n", mtd);
}
else if (0 == strcmp(option_str[i], "--smr-multi")){
ssmrflg=true;
printf("--smr-multi \n");
}
else if (0 == strcmp(option_str[i], "--smr-ivw")){
ssmrivwflg=true;
printf("--smr-ivw \n");
}
else if (0 == strcmp(option_str[i], "--smr-ivw-trans")){
ssmrivwtransflg=true;
printf("--smr-ivw-trans \n");
}
else if (0 == strcmp(option_str[i], "--smr-gwas-to-gwas")){
ssmrgwastogwasflg=true;
printf("--smr-gwas-to-gwas \n");
}
else if (0 == strcmp(option_str[i], "--smr-multi-rev")){
ssmrrevflg=true;
printf("--smr-multi-rev \n");
}
else if (0 == strcmp(option_str[i], "--ld-matrix")){
ldmatrix=true;
printf("--ld-matrix \n");
}
else if (0 == strcmp(option_str[i], "--ld-upper-limit")){
ld_prune = atof(option_str[++i]);
printf("--ld-upper-limit %f\n", ld_prune);
if(ld_prune<0 || ld_prune>1)
{
fprintf (stderr, "Error: --ld-upper-limit should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--ld-multi-snp")){
ld_prune_multi = atof(option_str[++i]);
printf("--ld-multi-snp %f\n", ld_prune_multi);
if(ld_prune_multi<0 || ld_prune_multi>1)
{
fprintf (stderr, "Error: --ld-multi-snp should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--smr")){
smr_flag=true;
printf("--smr \n");
}
else if (0 == strcmp(option_str[i], "--make-besd-dense")){
make_besd_flag=true;
save_dense_flag=true;
printf("--make-besd-dense \n");
}
else if(strcmp(option_str[i],"--cis-wind")==0){
cis_flag=true;
cis_itvl=atoi(option_str[++i]);
printf("--cis-wind %d Kb\n", cis_itvl);
if(cis_itvl<=0 )
{
fprintf (stderr, "Error: --cis-wind should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--trans-wind")==0){
trans_itvl=atoi(option_str[++i]);
printf("--trans-wind %d Kb\n", trans_itvl);
if(trans_itvl<0 )
{
fprintf (stderr, "Error: --trans-wind should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--peqtl-trans")==0){
transThres=atof(option_str[++i]);
printf("--peqtl-trans %10.2e\n", transThres);
if(transThres<0 || transThres>1)
{
fprintf (stderr, "Error: --peqtl-trans should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--peqtl-cis")==0){
cisThres=atof(option_str[++i]);
printf("--peqtl-cis %10.2e\n", cisThres);
if(cisThres<0 || cisThres>1)
{
fprintf (stderr, "Error: --peqtl-cis should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--peqtl-other")==0){
restThres=atof(option_str[++i]);
printf("--peqtl-other %10.2e\n", restThres);
if(restThres<0 || restThres>1)
{
fprintf (stderr, "Error: --peqtl-other should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--efile")){
eremlFlag=true;
eFileName = option_str[++i];
FLAG_VALID_CK("--efile", eFileName);
printf("--efile %s\n", eFileName);
}
else if (0 == strcmp(option_str[i], "--query")){
lookup_flag=true;
if(i+1==option_num || has_prefix(option_str[i+1],"--")) plookup = 5.0e-8;
else plookup = atof (option_str[++i]);
if(bldFileName) printf("--query\n");
else printf("--query %10.2e\n", plookup);
if(plookup<0 || plookup>1)
{
fprintf (stderr, "Error: --query should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if(0==strcmp(option_str[i],"--trans-dense")){
trans_dense=true;
printf("--trans-dense\n");
}
else if(strcmp(option_str[i],"--genes")==0){
genelistName=option_str[++i];
FLAG_VALID_CK("--genes", genelistName);
cout<<"--genes "<<genelistName<<endl;
CommFunc::FileExist(genelistName);
}
else if(strcmp(option_str[i],"--gene-list")==0){
geneAnnoName=option_str[++i];
FLAG_VALID_CK("--gene-list", geneAnnoName);
cout<<"--gene-list "<<geneAnnoName<<endl;
CommFunc::FileExist(geneAnnoName);
}
else if(strcmp(option_str[i],"--set-list")==0){
setlstName=option_str[++i];
FLAG_VALID_CK("--set-list", setlstName);
cout<<"--set-list "<<setlstName<<endl;
CommFunc::FileExist(setlstName);
}
else if (0 == strcmp(option_str[i], "--target-snp")){
refSNP = option_str[++i];
FLAG_VALID_CK("--target-snp", refSNP);
printf("--target-snp %s\n", refSNP);
}
else if (0 == strcmp(option_str[i], "--heidi-off")){
heidioffFlag = true;
printf("--heidi-off \n");
}
else if(0 == strcmp(option_str[i],"--thread-num")){
thread_num=atoi(option_str[++i]);
printf("--thread-num %d\n", thread_num);
}
else if (0 == strcmp(option_str[i], "--besd-flist")){
combineFlg=true;
eqtlsmaslstName = option_str[++i];
FLAG_VALID_CK("--besd-flist", eqtlsmaslstName);
printf("--besd-flist %s\n", eqtlsmaslstName);
CommFunc::FileExist(eqtlsmaslstName);
}
else if (0 == strcmp(option_str[i], "--plot")){
plotflg = true;
printf("--plot \n" );
}
else if (0 == strcmp(option_str[i], "--trans")){
smr_trans_flag = true;
if(!cis_flag) cis_itvl=5000;
printf("--trans \n" );
}
else if (0 == strcmp(option_str[i], "--eqtl-flist")){
syllabusName = option_str[++i];
gctaflag = true;
if(syllabusName !=NULL && has_prefix(syllabusName, "--"))
{
syllabusName=NULL;
i--;
}else printf("--eqtl-flist %s\n", syllabusName);
}
else if (0 == strcmp(option_str[i], "--smr-format")){
gctaflag = true;
printf("--smr-format \n" );
}
else if (0 == strcmp(option_str[i], "--plink-qassoc-format")){
plinkflag = true;
gctaflag = false;
printf("--plink-qassoc-format \n" );
}
else if (0 == strcmp(option_str[i], "--gemma-format")){
gemmaflag = true;
gctaflag = false;
printf("--gemma-format \n" );
}
else if (0 == strcmp(option_str[i], "--bolt-assoc-format")){
boltflag = true;
gctaflag = false;
printf("--bolt-assoc-format \n" );
}
else if (0 == strcmp(option_str[i], "--geno-uni")){
genouni = true;
printf("--geno-uni \n" );
}
else if (0 == strcmp(option_str[i], "--merlin-fastassoc-format")){
merlinflag = true;
gctaflag = false;
printf("--merlin-fastassoc-format \n" );
}
else if (0 == strcmp(option_str[i], "--matrix-eqtl-format")){
mateqtlflag = true;
gctaflag = false;
printf("--matrix-eqtl-format \n" );
}
else if (0 == strcmp(option_str[i], "--fastqtl-nominal-format")){
fastqtlnflag = true;
gctaflag = false;
printf("--fastqtl-nominal-format \n" );
}
else if (0 == strcmp(option_str[i], "--fastqtl-permu-format")){
fastqtlpflag = true;
gctaflag = false;
printf("--fastqtl-permu-format \n" );
}
else if(strcmp(option_str[i],"--extract-trait")==0){
traitlstName=option_str[++i];
FLAG_VALID_CK("--extract-trait", traitlstName);
cout<<"--extract-trait "<<traitlstName<<endl;
CommFunc::FileExist(traitlstName);
}
else if(strcmp(option_str[i],"--esd-std")==0){
esdstd=true;
cout<<"--esd-std "<<endl;
}
else if(strcmp(option_str[i],"--update-freq")==0){
freqName=option_str[++i];
FLAG_VALID_CK("--update-freq", freqName);
cout<<"--update-freq "<<freqName<<endl;
CommFunc::FileExist(freqName);
}
else if(strcmp(option_str[i],"--probe-var")==0){
vpFileName=option_str[++i];
FLAG_VALID_CK("--probe-var", vpFileName);
cout<<"--probe-var "<<vpFileName<<endl;
CommFunc::FileExist(vpFileName);
}
else if(strcmp(option_str[i],"--meta")==0){
metaflg=true;
combineFlg=false;
smr_flag=false;
cout<<"--meta "<<endl;
}
else if(0==strcmp(option_str[i],"--mecs")){
metaflg=true;
meta_mtd=1;
printf("--mecs\n");
}
else if(0==strcmp(option_str[i],"--pmecs")){
pmecs=atof(option_str[++i]);
if (pmecs < 0 || pmecs > 1) {
printf("\nError: --pmecs should be between 0 to 1.\n");
exit (EXIT_FAILURE);
}
printf("--pmecs %0.2e\n", pmecs);
}
else if(0==strcmp(option_str[i],"--nmecs")){
nmecs=atoi(option_str[++i]);
if (nmecs <= 0 ) {
printf("\nError: --nmecs should be over 0.\n");
exit (EXIT_FAILURE);
}
printf("--nmecs %d\n", nmecs);
}
else if(strcmp(option_str[i],"--smr-wind")==0){
if(smr_trans_flag)
{
trans_itvl=atoi(option_str[++i]);
printf("--smr-wind %d Kb\n", trans_itvl);
if(trans_itvl<0 )
{
fprintf (stderr, "Error: --smr-wind should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else
{
cis_itvl=atoi(option_str[++i]);
printf("--smr-wind %d Kb\n", cis_itvl);
if(cis_itvl<0 )
{
fprintf (stderr, "Error: --smr-wind should be over 0.\n");
exit (EXIT_FAILURE);
}
}
}
else if(strcmp(option_str[i],"--outcome-wind")==0){
outcomePrbWind=atoi(option_str[++i]);
printf("--outcome-wind %d Kb\n", outcomePrbWind);
if(outcomePrbWind<0 )
{
fprintf (stderr, "Error: --outcome-wind should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--set-wind")==0){
setWind=atoi(option_str[++i]);
printf("--set-wind %d kb\n", setWind);
if(setWind<=0 )
{
fprintf (stderr, "Error: --set-wind should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--est-n")==0){
est_effe_spl_size_flg=true;
combineFlg=false;
cout<<"--est-n "<<endl;
}
else if(strcmp(option_str[i],"--smr-file")==0){
smrRltFileName=option_str[++i];
FLAG_VALID_CK("--smr-file", smrRltFileName);
cout<<"--smr-file "<<smrRltFileName<<endl;
CommFunc::FileExist(smrRltFileName);
}
else if(strcmp(option_str[i],"--recode")==0){
recodeflg=true;
cout<<"--recode "<<endl;
}
else if(strcmp(option_str[i],"--chr")==0){
char* tmpstr=option_str[++i];
if(strncmp(tmpstr,"X",1)==0) chr=23;
else if(strncmp(tmpstr,"Y",1)==0) chr=24;
else chr=atoi(tmpstr);
FLAG_VALID_CK("--chr", tmpstr);
cout<<"--chr "<<tmpstr<<endl;
}
else if(strcmp(option_str[i],"--probe-chr")==0){
char* tmpstr=option_str[++i];
if(strncmp(tmpstr,"X",1)==0) prbchr=23;
else if(strncmp(tmpstr,"Y",1)==0) prbchr=24;
else prbchr=atoi(tmpstr);
FLAG_VALID_CK("--probe-chr", tmpstr);
cout<<"--probe-chr "<<tmpstr<<endl;
}
else if(strcmp(option_str[i],"--snp-chr")==0){
char* tmpstr=option_str[++i];
if(strncmp(tmpstr,"X",1)==0) snpchr=23;
else if(strncmp(tmpstr,"Y",1)==0) snpchr=24;
else snpchr=atoi(tmpstr);
FLAG_VALID_CK("--snp-chr", tmpstr);
cout<<"--snp-chr "<<tmpstr<<endl;
}
else if(strcmp(option_str[i],"--snp-rm")==0){
snp2rm=option_str[++i];
FLAG_VALID_CK("--snp-rm", snp2rm);
printf("--snp-rm %s\n", snp2rm);
}
else if (0 == strcmp(option_str[i], "--snp")){
snprs = option_str[++i];
FLAG_VALID_CK("--snp", snprs);
printf("--snp %s\n", snprs);
}
else if (0 == strcmp(option_str[i], "--from-snp")){
fromsnprs = option_str[++i];
FLAG_VALID_CK("--from-snp", fromsnprs);
printf("--from-snp %s\n", fromsnprs);
}
else if (0 == strcmp(option_str[i], "--to-snp")){
tosnprs = option_str[++i];
FLAG_VALID_CK("--to-snp", tosnprs);
printf("--to-snp %s\n", tosnprs);
}
else if (0 == strcmp(option_str[i], "--probe")){
prbname = option_str[++i];
FLAG_VALID_CK("--probe", prbname);
printf("--probe %s\n", prbname);
}
else if (0 == strcmp(option_str[i], "--from-probe")){
fromprbname = option_str[++i];
FLAG_VALID_CK("--from-probe", fromprbname);
printf("--from-probe %s\n", fromprbname);
}
else if (0 == strcmp(option_str[i], "--to-probe")){
toprbname = option_str[++i];
FLAG_VALID_CK("--to-probe", toprbname);
printf("--to-probe %s\n", toprbname);
}
else if(strcmp(option_str[i],"--snp-wind")==0){
snpwindFlag=true;
char* tmpstr=option_str[++i];
if(tmpstr==NULL || SMRDATA::has_prefix(tmpstr, "--")) i--;
else snpWind=atoi(tmpstr);
printf("--snp-wind %d Kb\n", snpWind);
if(snpWind<0 )
{
fprintf (stderr, "Error: --snp-wind should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--probe-wind")==0){
prbwindFlag=true;
char* tmpstr=option_str[++i];
if(tmpstr==NULL || SMRDATA::has_prefix(tmpstr, "--")) i--;
else prbWind=atoi(tmpstr);
printf("--probe-wind %d Kb\n", prbWind);
if(prbWind<0 )
{
fprintf (stderr, "Error: --probe-wind should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--gene")){
genename = option_str[++i];
FLAG_VALID_CK("--gene", genename);
printf("--gene %s\n", genename);
}
else if(strcmp(option_str[i],"--from-snp-kb")==0){
fromsnpkb=atoi(option_str[++i]);
printf("--from-snp-kb %d Kb\n", fromsnpkb);
if(fromsnpkb<0 )
{
fprintf (stderr, "Error: --from-snp-kb should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--to-snp-kb")==0){
tosnpkb=atoi(option_str[++i]);
printf("--to-snp-kb %d Kb\n", tosnpkb);
if(tosnpkb<0 )
{
fprintf (stderr, "Error: --to-snp-kb should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--from-probe-kb")==0){
fromprbkb=atoi(option_str[++i]);
printf("--from-probe-kb %d Kb\n", fromprbkb);
if(fromprbkb<0 )
{
fprintf (stderr, "Error: --from-probe-kb should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--to-probe-kb")==0){
toprbkb=atoi(option_str[++i]);
printf("--to-probe-kb %d Kb\n", toprbkb);
if(toprbkb<0 )
{
fprintf (stderr, "Error: --to-probe-kb should be over 0.\n");
exit (EXIT_FAILURE);
}
}
else if(strcmp(option_str[i],"--extract-single-exposure-probe")==0){
eprobe=option_str[++i];
FLAG_VALID_CK("--extract-single-exposure-probe", eprobe);
cout<<"--extract-single-exposure-probe "<<eprobe<<endl;
}
else if(strcmp(option_str[i],"--extract-single-outcome-probe")==0){
oprobe=option_str[++i];
FLAG_VALID_CK("--extract-single-outcome-probe", oprobe);
cout<<"--extract-single-outcome-probe "<<oprobe<<endl;
}
else if(strcmp(option_str[i],"--exclude-single-exposure-probe")==0){
eprobe2rm=option_str[++i];
FLAG_VALID_CK("--exclude-single-exposure-probe", eprobe2rm);
cout<<"--exclude-single-exposure-probe "<<eprobe2rm<<endl;
}
else if(strcmp(option_str[i],"--exclude-single-outcome-probe")==0){
oprobe2rm=option_str[++i];
FLAG_VALID_CK("--exclude-single-outcome-probe", oprobe2rm);
cout<<"--exclude-single-outcome-probe "<<oprobe2rm<<endl;
}
else if(0==strcmp(option_str[i],"--qfile")){
queryfileflg=true;
queryFileName=option_str[++i];
FLAG_VALID_CK("--qfile", queryFileName);
printf("--qfile %s\n",queryFileName);
}
else if(strcmp(option_str[i],"--beqtl-qc")==0){
qcflag=true;
qcmtd = atoi(option_str[++i]);
if(qcmtd<0 || qcmtd>2)
{
fprintf (stderr, "Error: --beqtl-qc should be 0,1 or 2.\n"); // 1 for SD, 2 for MAD
exit (EXIT_FAILURE);
}
cout<<"--beqtl-qc "<<qcmtd<<endl;
}
else if(strcmp(option_str[i],"--z-thresh")==0){
z_thresh = atoi(option_str[++i]);
if(z_thresh<0 )
{
fprintf (stderr, "Error: --z-thresh should be positive.\n");
exit (EXIT_FAILURE);
}
cout<<"--z-thresh "<<z_thresh<<endl;
}
else if (0 == strcmp(option_str[i], "--psmr")){
threshpsmrest = atof(option_str[++i]);
printf("--psmr %10.2e\n", threshpsmrest);
if(threshpsmrest<0 || threshpsmrest>1)
{
fprintf (stderr, "Error: --psmr should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if (0 == strcmp(option_str[i], "--phet")){
threshphet = atof(option_str[++i]);
printf("--phet %10.2e\n", threshphet);
if(threshphet<0 || threshphet>1)
{
fprintf (stderr, "Error: --phet should be within the range from 0 to 1.\n");
exit (EXIT_FAILURE);
}
}
else if(0==strcmp(option_str[i],"--descriptive-cis")){
count_cis_flag=true;
printf("--descriptive-cis\n");
}
else if(0==strcmp(option_str[i],"--descriptive-trans")){
count_trans_flag=true;
if(!cis_flag) cis_itvl=5000;