multiReader::multiReader(int argc,char**argv){
gz=Z_NULL;
myglf=NULL;myvcf=NULL;mpil=NULL;bglObj=NULL;
nLines=50;
fname=NULL;
intName=1;
minQ = MINQ;
nInd =0;
isSim =0;
args=NULL;
args = setArgStruct(argc,argv);
fprintf(args->argumentFile,"\t-> Command: \n");
for(int i=0;i<argc;i++)
fprintf(args->argumentFile,"%s ",argv[i]);
// fprintf(args->argumentFile,"\n\n");
if(args->argumentFile!=stderr)
fprintf(args->argumentFile,"\n\t-> angsd version: %s (htslib: %s) build(%s %s)\n",ANGSD_VERSION,hts_version(),__DATE__,__TIME__);
void printTime(FILE *fp);
printTime(args->argumentFile);
//type = args->inputtype;
if(args->argc==2) {
if((!strcasecmp(args->argv[1],"-beagle")) ||
(!strcasecmp(args->argv[1],"-glf")) ||
(!strcasecmp(args->argv[1],"-glf3")) ||
(!strcasecmp(args->argv[1],"-pileup")) ||
(!strcasecmp(args->argv[1],"-vcf-GL")) ||
(!strcasecmp(args->argv[1],"-vcf-pl")) ||
(!strcasecmp(args->argv[1],"-glf10_text")) ||
(!strcasecmp(args->argv[1],"-vcf-GP"))) {
printArg(stdout,args);
exit(0);
}else if ((!strcasecmp(args->argv[1],"-bam")) ||
(!strcasecmp(args->argv[1],"-b"))){
setArgsBam(args);
exit(0);
}else
return;
}
getOptions(args);
if(args->fai==NULL){
int printAndExit =0;
switch(args->inputtype)
{
case INPUT_GLF:
printAndExit=1;
break;
case INPUT_GLF10_TEXT:
printAndExit=1;
break;
case INPUT_GLF3:
printAndExit=1;
break;
case INPUT_BEAGLE:
printAndExit=1;
break;
case INPUT_PILEUP:
printAndExit=1;
break;
}
if(printAndExit){
fprintf(stderr,"\t-> Must supply -fai file\n");
exit(0);
}
}
if(args->fai){
if(!(args->hd=getHeadFromFai(args->fai)))
exit(0);
}else{
if(args->nams.size()==0){
fprintf(stderr,"\t-> Must choose inputfile -bam/-glf/-glf3/-pileup/-i/-vcf-gl/-vcf-gp/-vcf-pl/-glf10_text filename\n");
exit(0);
}
if(args->inputtype==INPUT_BAM){
htsFile *in=sam_open(args->nams[0],"r");
assert(in);
args->hd= sam_hdr_read(in);
hts_close(in);
}
}
if(!(INPUT_VCF_GL||INPUT_VCF_GP)){
if(args->hd==NULL){
fprintf(stderr,"For non-bams you should include -fai arguments\n");
exit(0);
}
}
if((args->inputtype==INPUT_PILEUP||args->inputtype==INPUT_GLF||args->inputtype==INPUT_GLF3||args->inputtype==INPUT_GLF10_TEXT)){
if(nInd==0){
fprintf(stderr,"\t-> Must supply -nInd when using -glf/-glf3/-pileup/-glf10_text files\n");
exit(0);
}
}else
args->nInd = args->nams.size();
if(args->inputtype==INPUT_VCF_GP||args->inputtype==INPUT_VCF_GL){
if(args->regions.size()>1){
fprintf(stderr,"\t-> Only one region can be specified with using bcf (i doubt more is needed) will exit\n");
exit(0);
}else if(args->regions.size()<=1){
myvcf = new vcfReader(args->infile,NULL);
args->hd=bcf_hdr_2_bam_hdr_t(myvcf->hs);
args->nInd = myvcf->hs->nsamples;
}
}
//make args->hd
revMap = buildRevTable(args->hd);
args->revMap = revMap;
setArgsBam(args);
if(args->inputtype==INPUT_VCF_GL){
if(args->regions.size()==1){
char tmp[1024];
int start=args->regions[0].start;
int stop=args->regions[0].stop;
int ref=args->regions[0].refID;
snprintf(tmp,1024,"%s:%d-%d",args->hd->target_name[ref],start+1,stop);
// fprintf(stderr,"tmp:%s\n",tmp);
// exit(0);
myvcf->seek(tmp);
}
}
if(fname==NULL)
return;
gz=Z_NULL;
gz=gzopen(fname,"r");
if(gz==Z_NULL){
fprintf(stderr,"\t-> Problem opening file: \'%s\'\n",fname);
exit(0);
}
switch(args->inputtype){
case INPUT_PILEUP:{
mpil = new mpileup(args->nInd,gz,args->revMap,minQ);
break;
}
case INPUT_GLF:{
myglf = new glfReader(args->nInd,gz,10,isSim);
break;
}
case INPUT_GLF3:{
isSim = 1; //Added by FGV on 22/02/2015: GLF3 is always simulated data until a better alternative can be found
myglf = new glfReader(args->nInd,gz,3,isSim);
break;
}
case INPUT_GLF10_TEXT:{
myglf_text = new glfReader_text(args->nInd,gz,args->revMap);
break;
}
case INPUT_BEAGLE:{
bglObj = new beagle_reader(gz,args->revMap,intName,args->nInd);
break;
}
default:{
break;
}
}
if(args->inputtype==INPUT_VCF_GL||args->inputtype==INPUT_VCF_GL){
fprintf(stderr,"\t-> VCF still beta. Remember that\n");
fprintf(stderr,"\t 1. indels are are discarded\n");
fprintf(stderr,"\t 2. will use chrom, pos PL columns\n");
fprintf(stderr,"\t 3. GL tags are interpreted as log10 and are scaled to ln (NOT USED)\n");
fprintf(stderr,"\t 4. GP tags are interpreted directly as unscaled post probs (spec says phredscaled...) (NOT USED)\n");
fprintf(stderr,"\t 5. FILTER column is currently NOT used (not sure what concensus is)\n");
fprintf(stderr,"\t 6. -sites does NOT work with vcf input but -r does\n");
fprintf(stderr,"\t 7. vcffilereading is still BETA, please report strange behaviour\n");
}
}
multiReader::multiReader(int argc,char**argv){
fai = NULL;
bytesPerLine = 33554432 ;//2^15 about 33 megs perline/persites should be enough
nLines=50;
fname=NULL;
intName=1;
minQ = MINQ;
nInd =0;
nInd2=-1;
from =to=-1;
isSim =0;
args=NULL;
args = setArgStruct(argc,argv);
fprintf(args->argumentFile,"\t-> Command: \n");
for(int i=0;i<argc;i++)
fprintf(args->argumentFile,"%s ",argv[i]);
// fprintf(args->argumentFile,"\n\n");
extern double VERS;
fprintf(args->argumentFile,"\n\t-> angsd version: %.3f\t build(%s %s)\n",VERS,__DATE__,__TIME__);
void printTime(FILE *fp);
printTime(args->argumentFile);
type = args->inputtype;
if(args->argc==2){
if((!strcasecmp(args->argv[1],"-beagle"))||!strcasecmp(args->argv[1],"-glf")||(!strcasecmp(args->argv[1],"-pileup"))){
printArg(stdout);
exit(0);
}else if ((!strcasecmp(args->argv[1],"-bam"))|| (!strcasecmp(args->argv[1],"-b"))){
setArgsBam(args);
exit(0);
}else
return;
}
getOptions(args);
if(fai){
hd=getHeadFromFai(fai);
}else{
if(args->nams.size()==0){
fprintf(stderr,"\t-> Must choose inputfile -bam/-glf/-pileup/-i filename\n");
exit(0);
}
hd= getHd_andClose(args->nams[0]);
}
args->hd = hd;
if(args->hd==NULL){
fprintf(stderr,"For non-bams you should include -fai arguments\n");
exit(0);
}
if((type==INPUT_PILEUP||type==INPUT_GLF)){
if(nInd==0){
fprintf(stderr,"\t-> Must supply -nInd when using raw GLF files\n");
exit(0);
}
}else
args->nInd = args->nams.size();
revMap = buildRevTable(args->hd);
args->revMap = revMap;
setArgsBam(args);
if(fname==NULL)
return;
gz=gzopen(fname,"r");
switch(type){
case INPUT_PILEUP:{
mpil = new mpileup(args->nInd,gz,bytesPerLine,args->revMap,minQ);
break;
}
case INPUT_GLF:{
myglf = new glfReader(args->nInd,nInd2,from,to,gz,isSim);
break;
}
case INPUT_BEAGLE:{
bglObj = new beagle_reader(bytesPerLine,gz,args->revMap,intName,args->nInd);
break;
}
default:{
// fprintf(stderr,"\t[%s] assuming what ?\n",__FUNCTION__);
//pl = new pileups (faifile,lStart,lStop,filenames,type);
break;
}
}
}
