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beagleReader.cpp
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beagleReader.cpp
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#include "analysisFunction.h"
#include "beagleReader.h"
#include "aio.h"
beagle_reader::~beagle_reader(){
free(buffer);
free(buf);
}
beagle_reader::beagle_reader(gzFile gz_a,const aMap *revMap_a,int intName_a,int &nInd_a){
gz=gz_a;
revMap=revMap_a;
l=128;
intName = intName_a;
original=buffer=(char *) calloc(l,sizeof(char));
buf=(char *) calloc(l,sizeof(char));
const char *delims = "\t \n";
int nCol=1;
int presize=l;
aio::tgets(gz,&buffer,&l);
if(buffer!=original)
original=buffer;
if(l>presize){
buf=(char*)realloc(buf,strlen(buffer)+1);
presize=l;
}
strtok_r(buffer,delims,&buffer);
while(strtok_r(NULL,delims,&buffer))
nCol++;
if(nCol % 3 ){
fprintf(stderr,"\t-> Number of columns should be a multiple of 3, nCol=%d\n",nCol);
exit(0);
}
nInd_a=nCol/3-1;
nInd = nInd_a;
}
void parsepost(char *buffer,double *post,int nInd,const char *delims){
for(int i=0;i<nInd*3;i++){
char *tsk = strtok_r(NULL,delims,&buffer);
aio::doAssert(tsk!=NULL,1,AT,"");
post[i] = atof(tsk);
}
}
//parse beagle fields
//
//chr_A_B_C -> chr: chr_A_B ; pos: C
//bpost = to give parsepost
//bufpos = position info
//buf = contig id
//bufmaj = major
//bufmin = minor
void parse_beagle_fields(char *buffer, char **buf, char **bufpos, char **bufmaj, char **bufmin, char **bpost,const char *delims){
// copy buffer to working buffer buf
// we need to keep buffer as it is
// size of buf is reallocated together with buffer
// buff is cleaned together with buffer
strcpy(*buf,buffer);
char *a;
//line= chr_a_b_123 g c 0.05 0.05 0.05
//point to the first delim
//a=chr_a_b_123
a = strtok_r(*buf,delims,bpost);
//bpost is now after first delim
//bpost=g c 0.05 0.05 0.05
// fprintf(stderr,"\n\nbpost=%s\n",*bpost);
if ((a=strrchr(a,'_'))!=NULL){
//a= _123
//a+1= 123
*bufpos=a+1;
//bufpos now stores the position info=123
}
//here buf=chr_a_b_123
//terminate after contig id
//write \0 to the start of position info
*strrchr(*buf,'_')='\0';
//here buf now contains contig id=chr_a_b
//extract major and minor from bpost
*bufmaj=&refToChar[strtok_r(*bpost,delims,bpost)[0]];
*bufmin=&refToChar[strtok_r(NULL,delims,bpost)[0]];
}
funkyPars *beagle_reader::fetch(int chunksize){
static const char *delims = "\t \n";
double **post = new double*[chunksize];
// double **postbuf = new double*[chunksize];
char *bufpos;
char *bufmaj;
char *bufmin;
char *bpost;
funkyPars * myfunky =funkyPars_init();
myfunky->posi = new int[chunksize];
myfunky->major = new char[chunksize];
myfunky->minor = new char[chunksize];
for(int s=0;s<chunksize;s++){
post[s] = new double[nInd*3];
}
int nSites=0;
static int positions =0;//every site is a new position across different chunks
static int lastRefId =-1;
static int changed =0;
READAGAIN:
if(changed){
//parse an entire site:
// fprintf(stdout,"nSites %d\n",nSites);
myfunky->refId = lastRefId;
parse_beagle_fields(buffer,&buf,&bufpos,&bufmaj,&bufmin,&bpost,delims);
myfunky->posi[nSites] = atoi(bufpos)-1;
myfunky->major[nSites] = *bufmaj;
myfunky->minor[nSites] = *bufmin;
parsepost(bpost,post[nSites],nInd,delims);
nSites++;
changed =0;
}
buffer=original;
int presize=l;
while(aio::tgets(gz,&buffer,&l)) {
if(l>presize){
buf=(char*)realloc(buf,strlen(buffer)+1);
presize=l;
}
if(buffer!=original)
original=buffer;
if(intName){
//identifier is chr_pos or snp name
parse_beagle_fields(buffer,&buf,&bufpos,&bufmaj,&bufmin,&bpost,delims);
//buf now contains contig id
aMap ::const_iterator it = revMap->find(buf);
if(it==revMap->end()){
fprintf(stderr,"\t-> Problem finding chr:%s from faifile\n",buf);
exit(0);
}
if(lastRefId==-1){
lastRefId = it->second;
}
if(lastRefId!=it->second){
changed =1;
lastRefId = it->second;
if(nSites==0){// if chromosome if finish then read next one
goto READAGAIN;
}
break;
}
lastRefId = it->second;
myfunky->refId = lastRefId;
myfunky->posi[nSites] = atoi(bufpos)-1;
}
else{
parse_beagle_fields(buffer,&buf,&bufpos,&bufmaj,&bufmin,&bpost,delims);
myfunky->refId = 0;
myfunky->posi[nSites] = positions++;
}
myfunky->major[nSites] = *bufmaj;
myfunky->minor[nSites] = *bufmin;
parsepost(bpost,post[nSites],nInd,delims);
buffer=original;
nSites++;
if(nSites>=chunksize)
break;
}
if(nSites<chunksize){
for(int s=nSites;s<chunksize;s++)
delete[] post[s];
}
myfunky->nInd=nInd;
myfunky->post=post;
myfunky->numSites = nSites;
if(nSites==0 & changed==0){
fprintf(stdout,"Done reading beagle\n");
funkyPars_destroy(myfunky);
return(NULL);
}
return(myfunky);
}