hwe::hwe(const char *outfiles,argStruct *arguments,int inputtype){
doHWE=0;
if(arguments->argc==2){
if(!strcmp(arguments->argv[1],"-doHWE")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
printArg(arguments->argumentFile);
if(doHWE==0)
return;
//make output files
const char* postfix;
postfix=".hwe.gz";
if(doHWE>0){
outfileZ = openFileGz(outfiles,postfix,GZOPT);
//print header
gzprintf(outfileZ,"Chromo\tPosition\tMajor\tMinor\tFreq\thweFreq\tF\tLRT\n");
}
}
abbababa::abbababa(const char *outfiles,argStruct *arguments,int inputtype){
doAbbababa=0;
minQ=MINQ;//<-general.h
sample=1;
currentChr=-1;
if(arguments->argc==2){
if(!strcmp(arguments->argv[1],"-doAbbababa")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
printArg(arguments->argumentFile);
if(doAbbababa==0)
return;
//make output files
const char* postfix;
postfix=".abbababa.gz";
outfileZ = openFileGz(outfiles,postfix,GZOPT);
const char* postfix2;
postfix2=".abbababa2";
outfile = openFile(outfiles,postfix2);
//allocate allele counts
alleleCounts = new size_t *[nInd];
for(int i=0;i<nInd;i++)
alleleCounts[i] = new size_t [256];
for(int i=0;i<nInd;i++)
for(int j=0;j<256;j++)
alleleCounts[i][j]=0;
alleleCountsChr = new size_t *[nInd];
for(int i=0;i<nInd;i++)
alleleCountsChr[i] = new size_t [256];
for(int i=0;i<nInd;i++)
for(int j=0;j<256;j++)
alleleCountsChr[i][j]=0;
}
likeClass::likeClass(const char *outfiles,argStruct *arguments,int inputtype){
postfix = ".glf.gz";
beaglepostfix = ".beagle.gz";
trim =0;
GL=0;
doGlf=0;
errorFname = NULL;
errorProbs = NULL;
GL=0;
minQ = MINQ;//<- general.h
minInd=0;
angsd_tmpdir = strdup("angsd_tmpdir");
if(arguments->argc==2){
if(!strcmp(arguments->argv[1],"-GL")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
printArg(arguments->argumentFile);
// if(GL==0)
// return;
if(GL==1)
bam_likes_init();
else if(GL==2)
gatk_init();
else if(GL==3){
soap.init(arguments->nInd,angsd_tmpdir);
if(soap.doRecal)
fprintf(stderr,"[%s] Will calculate recalibration matrices, please don't do any other analysis\n",__FILE__);
else
fprintf(stderr,"[%s] Will use precalculated calibration matrices\n",__FILE__);
}else if(GL==4) {
//default errormatrix
double errorsDefault[4][4]={{0 ,0.00031 , 0.00373 , 0.000664},
{0.000737, 0 , 0.000576, 0.001702},
{0.001825,0.000386, 0 , 0.000653},
{0.00066 ,0.003648, 0.000321, 0 },
};
//allocate and plug in default values
errors = new double *[4];
for(int i=0;i<4;i++){
errors[i] = new double[4];
for(int j=0;j<4;j++)
errors[i][j] = errorsDefault[i][j];
}
if(errorFname!=NULL)
readError(errors,errorFname);
errorProbs = error::generateErrorPointers(errors,3,4);
}
gzoutfile = Z_NULL;
bufstr.s=NULL; bufstr.l=bufstr.m=0;// <- used for buffered output
bufstr.l=0;
if(doGlf){
if(doGlf!=2)
gzoutfile = openFileGz(outfiles,postfix,GZOPT);
else{
gzoutfile = openFileGz(outfiles,beaglepostfix,GZOPT);
kputs("marker\tallele1\tallele2",&bufstr);
for(int i=0;i<arguments->nInd;i++){
kputs("\tInd",&bufstr);
kputw(i,&bufstr);
kputs("\tInd",&bufstr);
kputw(i,&bufstr);
kputs("\tInd",&bufstr);
kputw(i,&bufstr);
}
kputc('\n',&bufstr);
gzwrite(gzoutfile,bufstr.s,bufstr.l);
}
}
}
//constructor
frequency::frequency(const char *outfiles,argStruct *arguments,int inputtype){
inputIsBeagle =0;
filtLrt=filtMaf =0;
minMaf =0.01;
minLRT =24;
nInd = arguments->nInd;
eps = 0.001;
doZ =0;
outfile = Z_NULL;
doMaf=0;
GL=0;
doSNP=0;
doPost=0;
emIter=100;
doMajorMinor=0;
refName = NULL;
ancName = NULL;
EM_START = 0.001;
if(arguments->argc==2){
if(!strcmp(arguments->argv[1],"-doMaf")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
printArg(arguments->argumentFile);
if(doMaf==0)
return;
//make output files
const char* postfix;
if(doZ==1){
postfix=".mafs.gz";
outfileZ = openFileGz(outfiles,postfix,"w6h");
}else{
postfix=".mafs";
outfile = openFile(outfiles,postfix);
}
//print header
kstring_t bufstr;
bufstr.s=NULL;bufstr.l=bufstr.m=0;
kputs("chromo\tposition\tmajor\tminor\t",&bufstr);
if(refName!=NULL||inputtype==3)// inputtyp=3 is tglf, if tglf then -posi has been supplied
kputs("ref\t",&bufstr);
if(ancName||inputtype==3||inputtype==4)// inputtyp=3 is tglf, if tglf then -posi has been supplied
kputs("anc\t",&bufstr);
if(doMaf &1)
kputs("knownBFGS\t",&bufstr);
if(doMaf &2)
kputs("knownEM\t",&bufstr);
if(doMaf &4)
kputs("unknownBFGS\t",&bufstr);
if(doMaf &8)
kputs("unknownEM\t",&bufstr);
if(doMaf &16)
kputs("PPmaf\t",&bufstr);
if(doMaf &32)
kputs("phat\t",&bufstr);
if(doSNP){
if(doMaf &1)
kputs("pK-BFGS\t",&bufstr);
if(doMaf &2)
kputs("pK-EM\t",&bufstr);
if(doMaf &4)
kputs("pU-BFGS\t",&bufstr);
if(doMaf &8)
kputs("pu-EM\t",&bufstr);
}
kputs("nInd\n",&bufstr);
if(doZ==1)
gzwrite(outfileZ,bufstr.s,bufstr.l);
else
fprintf(outfile,"%s",bufstr.s);
free(bufstr.s);
}
int main(int argc, char **argv){
fprintf(stderr,"NGSrelate buildtime: (%s:%s)\n",__DATE__,__TIME__);
if(argc==1){// if no arguments, print info on program
info();
return 0;
}
//below for catching ctrl+c, and dumping files
struct sigaction sa;
sigemptyset (&sa.sa_mask);
sa.sa_flags = 0;
sa.sa_handler = handler;
sigaction(SIGPIPE, &sa, 0);
sigaction(SIGINT, &sa, 0);
//initial values
char *bfile = NULL;
char *binfile = NULL;
char *outfiles = NULL;
double a,k0,k1,k2;
a=k0=k1=-1;
k2=0;
int calcA = 1;
//filter opts
double minMaf = 0.01;
char *freqfile =NULL;
// reading arguments
argv++;
while(*argv){
if(strcmp(*argv,"-beagle")==0 ) bfile=*++argv;
else if(strcmp(*argv,"-bin")==0 ) binfile=*++argv;
else if(strcmp(*argv,"-freqfile")==0 ) freqfile=*++argv;
else if(strcmp(*argv,"-outnames")==0 ) outfiles=*++argv;
else if(strcmp(*argv,"-minMaf")==0 ) minMaf = atoi(*++argv);
else if(strcmp(*argv,"-a")==0 ) a = atof(*++argv);
else if(strcmp(*argv,"-k0")==0 ) k0 = atof(*++argv);
else if(strcmp(*argv,"-k1")==0 ) k1 = atof(*++argv);
else if(strcmp(*argv,"-k2")==0 ) k2 = atof(*++argv);
else if(strcmp(*argv,"-calcA")==0 ) calcA = atoi(*++argv);
else{
fprintf(stderr,"Unknown arg:%s\n",*argv);
info();
return 0;
}
++argv;
}
if(bfile==NULL&&binfile==NULL){
fprintf(stderr,"Please supply input data file: -beagle OR -bin");
info();
}else if(bfile!=NULL&&binfile!=NULL){
fprintf(stderr,"Please supply input data file: -beagle OR -bin");
info();
}
if(outfiles==NULL){
if(bfile!=NULL)
outfiles=bfile;
else
outfiles = binfile;
fprintf(stderr,"Will use: %s as prefix for output\n",outfiles);
}
FILE *flog=openFile(outfiles,".log");
clock_t t=clock();//how long time does the run take
time_t t2=time(NULL);
std::vector<perChr> pd;
if(bfile!=NULL){
bgl d=readBeagle(bfile);
fprintf(stderr,"Input beaglefile has dim: nsites=%d nind=%d\n",d.nSites,d.nInd);
pd = makeDat(d);
gzFile dfile = openFileGz(outfiles,".bin.gz","wb");
for(uint i=0;i<pd.size();i++)
marshall_dump(dfile,pd[i]);
gzclose(dfile);
}else{
gzFile dfile = getGz(binfile,"rb");
pd = marshall_read(dfile);
gzclose(dfile);
}
//calculate frequencies
for(uint i=0;i<pd.size();i++)
setFreq(pd[i]);
// printStuff(pd);
//set seed
srand(seed);
//below is the main looping trhought the iterations.
FILE *fp =openFile(outfiles,".freq");
for(int i=0;i<pd[0].nSites;i++)
fprintf(fp,"%f ",exp(pd[0].freq[i]));
fclose(fp);
double *freq = NULL;
if(freqfile!=NULL){
freq = readDouble(freqfile,pd[0].nSites);
fprintf(stderr,"freq=%f\n",freq[0]);
}
para p;
p.pair[0] = 0;p.pair[1] = 1;
p.a=a;p.k0=k0;p.k1=k1;p.k2=k2;
fprintf(stderr,"pa=%f pk0=%f\n",p.a,p.k0);
hmm res = analysis(pd[0],freq,p,calcA);
gzFile bo = openFileGz(outfiles,".bres.gz","wb");
fdump(bo,res,pd[0].name);
//deallocate memory
for(int i=0;1&&i<dumpedFiles.size();i++){
fprintf(stderr,"dumpedfiles are: %s\n",dumpedFiles[i]);
free(dumpedFiles[i]);
}
fprintf(stderr, "\t[ALL done] cpu-time used = %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
fprintf(stderr, "\t[ALL done] walltime used = %.2f sec\n", (float)(time(NULL) - t2));
// print to log file
fprintf(flog, "\t[ALL done] cpu-time used = %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
fprintf(flog, "\t[ALL done] walltime used = %.2f sec\n", (float)(time(NULL) - t2));
fclose(flog);
gzclose(bo);
return 0;
}
