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abcScounts.cpp
148 lines (120 loc) · 3.38 KB
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abcScounts.cpp
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#include <ctype.h>
#include "shared.h"
#include "analysisFunction.h"
#include "abcScounts.h"
#include "aio.h"
typedef unsigned char uchar;
typedef struct{
unsigned int rel_pos;
uchar A:2;
uchar C:2;
uchar G:2;
uchar T:2;
}counts;
aMap readvcf(const char *fname){
gzFile gz = Z_NULL;
gz=gzopen(fname,"rb");
if(gz==Z_NULL){
fprintf(stderr,"\t-> Problem opening file: %s\n",fname);
exit(0);
}
int at=0;
char buf[1024];
aMap am;
while(gzgets(gz,buf,1024)){
char chr[1024];
int pos;
char al1,al2;
if(4!=sscanf(buf,"%s\t%d\t%c\t%c\n",chr,&pos,&al1,&al2)){
fprintf(stderr,"\t-> problem parsing line: %d which looks like: %s\n",at,buf);
}
char tmpnam[2048];
snprintf(tmpnam,2048,"%s %d",chr,pos);
aMap::iterator it=am.find(tmpnam);
if(it!=am.end()){
fprintf(stderr,"\t-> Problem with duplicate positions: %s \n",tmpnam);
// exit(0);
}
am[strdup(tmpnam)]= at++;
}
fprintf(stderr,"\t-> read nsites from vcf:%lu\n",am.size());
return am;
}
void abcScounts::printArg(FILE *argFile){
fprintf(argFile,"------------------------\n%s:\n",__FILE__);
fprintf(argFile,"-doScounts\t%d \n",doScounts);
fprintf(argFile,"-vcfname\t%s \n",vcfname);
}
void abcScounts::getOptions(argStruct *arguments){
doScounts=angsd::getArg("-doScounts",doScounts,arguments);
vcfname = angsd::getArg("-vcfname",vcfname,arguments);
if(doScounts==0){
shouldRun[index]=0;
return;
}
}
abcScounts::abcScounts(const char *outfiles,argStruct *arguments,int inputtype){
vcfname = NULL;
doScounts = 0;
outfile = NULL;
if(arguments->argc==2){
if(!strcasecmp(arguments->argv[1],"-doScounts")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
if(doScounts==0)
return ;
printArg(arguments->argumentFile);
outfile = aio::openFileBG(outfiles,".scounts.gz");
if(!vcfname){
fprintf(stderr,"\t-> Must supply a file for screening\n");
exit(0);
}
int docounts =0;
docounts = angsd::getArg("-docounts",docounts,arguments);
if(docounts==0){
fprintf(stderr,"\t-> -doScounts requires -doCounts\n");
exit(0);
}
am = readvcf(vcfname);
}
abcScounts::~abcScounts(){
if(outfile!=NULL)
bgzf_close(outfile);
}
void abcScounts::clean(funkyPars *pars){
}
void abcScounts::print(funkyPars *pars){
if(doScounts==0)
return;
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]!=0){
char tmpname[1024];
sprintf(tmpname,"%s %d",header->target_name[pars->refId],pars->posi[s]+1);
aMap::iterator it = am.find(tmpname);
if(it==am.end()){
fprintf(stderr,"\t-> problem finding site: %s\n",tmpname);
continue;
}
counts cnts;
if(pars->counts[s][0]>3||pars->counts[s][1]>3||pars->counts[s][2]>3||pars->counts[s][3]>3){
fprintf(stderr,"\t-> skipping posi tmpname:%s du to depth>3\n",tmpname);
continue;
}
if(pars->counts[s][0]+pars->counts[s][1]+pars->counts[s][2]+pars->counts[3]==0)
continue;
cnts.rel_pos = it->second;
// fprintf(stderr,"realpos: %d rel_pos:%d\n",pars->posi[s]+1,it->second);
cnts.A = pars->counts[s][0];
cnts.C = pars->counts[s][1];
cnts.G = pars->counts[s][2];
cnts.T = pars->counts[s][3];
aio::doAssert(sizeof(counts)==bgzf_write(outfile,&cnts,sizeof(counts)*1),1,AT,"");
}
}
}
void abcScounts::run(funkyPars *pars){
}