abcGL::~abcGL(){
free(angsd_tmpdir);
if(GL==0&&doGlf==0)
return;
else if(GL==1)
bam_likes_destroy();
else if(GL==2)
gatk_destroy();
else if(GL==4)
abcError::killGlobalErrorProbs(errorProbs);
else if(GL==5)
phys_destroy();
if(doGlf) bgzf_close(gzoutfile);
if(gzoutfile!=NULL)
bgzf_close(gzoutfile2);
if(bufstr.s!=NULL)
free(bufstr.s);
if(errors){
for(int i=0;i<4;i++)
delete [] errors[i];
delete [] errors;
}
delete [] logfactorial;
}
likeClass::~likeClass(){
fflush(stderr);
free(angsd_tmpdir);
if(GL==0&&doGlf==0)
return;
else if(GL==1)
bam_likes_destroy();
else if(GL==2)
gatk_destroy();
else if(GL==4)
error::killGlobalErrorProbs(errorProbs);
if(doGlf) gzclose(gzoutfile);
if(bufstr.s!=NULL)
free(bufstr.s);
}
void call_bam(chunkyT *chk,double **lk,int trim){
// fprintf(stderr,"trim=%d\n",trim);
if(chk==NULL){
if(mod!=NULL)
bam_likes_destroy();
return;
}
assert(mod!=NULL);
for(int s=0;s<chk->nSites;s++){
//fprintf(stderr,"posi=%d\n",chk->nd[s][0].refPos);
lk[s] = new double[10*chk->nSamples];
for(int ii=0;ii<10*chk->nSamples;ii++)
lk[s][ii] = -0.0;
//fprintf(stderr,"chr=%s minbaseq=%d\n",chk->refName,minQ);
for(int i=0;i<chk->nSamples;i++){
tNode *nd = chk->nd[s][i];
if(nd==NULL)
continue;
uint16_t bases[nd->l];
int numItems =0;
for(int j=0;j<nd->l;j++) {
// fprintf(stderr,"posi=%d isop=%d +=%d\n",nd.posi[j],nd.isop[j],nd.posi[j]+nd.isop[j]);
int q=nd->qs[j];
// fprintf(stderr,"q=%c\n",q+33);
//fprintf(stderr,"skipping q=%d mapQ=%d posi=%d isop=%d\n",q,nd.mapQ[j],nd.posi[j],nd.isop[j]);
extern int minQ;
if(q<minQ || nd->posi[j]<trim||nd->isop[j]<trim){
// fprintf(stderr,"skipping q=%d mapQ=%d posi=%d isop=%d ind=%d\n",q,nd.mapQ[j],nd.posi[j],nd.isop[j],i);
continue;
}
/*
extern int minQ;
if(q<minQ || nd.posi[j]<trim||nd.isop[j]<trim){
// fprintf(stderr,"skipping q=%d mapQ=%d posi=%d isop=%d ind=%d\n",q,nd.mapQ[j],nd.posi[j],nd.isop[j],i);
continue;
}
*/
if (q>nd->mapQ[j])//dont allow qscores in read to exceed mapping quality
q=nd->mapQ[j];
if (q > 63) q = 63;
if (q < 4) q = 4;
// fprintf(stderr,"q=%d qshift=%d\n",q,q<<5);
//plug in values
// bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
int isLower = islower(nd->seq[j])>0;
//fprintf(stderr,"strandstuff=%d\tshiftstrandstuff=%d\n",isLower, isLower<<4 );
bases[numItems++] = q<<5 | isLower<<4 | refToInt[nd->seq[j]];
// fprintf(stderr,"bases[%d]=%d\n",j,bases[numItems-1]);
}
float likes[25];
for(int j=0;0&&j<25;j++)
likes[j]=0;
if(numItems!=0) {
errmod_cal(mod,numItems,5,bases,likes);
int ord[] = {0,1,2,3,6,7,8,12,13,18};
for(int gg=0;gg<10;gg++){
//fprintf(stderr,"%f\n",likes[ord[gg]]);
lk[s][i*10+gg] = -log(10.0) *likes[ord[gg]]/10.0;
}
}
}
// break;
}
}
