static int dma_r_ioctl(struct inode * inode, struct file * file, unsigned int cmd, unsigned long value) {
char * tmp;
unsigned long w4,adr,tmpval;
char val;
switch(cmd) {
case NUDAQ_2_START_DMA:
if (!dma_main_pointer){ nu2err=E_NU2_nopointer; return -EINVAL; }
if (dma_should_run) { nu2err=E_NU2_already_running; return -EINVAL;}
start_dma_engine();
break;
case NUDAQ_2_STOP_DMA:
if (!dma_main_pointer){ nu2err=E_NU2_nopointer; return -EINVAL; }
if (!dma_should_run) { nu2err=E_NU2_not_running; return -EINVAL;}
shutoff_dma_engine();
break;
case NUDAQ_2_READ_ERR:
return nu2err; break;
case NUDAQ_2_BYTES_READ:
return get_bytes_transfered();break;
case NUDAQ_2_OUTWORD:
outl(value,iocard_base+0x14);break;
case NUDAQ_2_READBACK:
return inl(iocard_base+0x14);break;
case NUDAQ_2_DITIMERS: /* set internal timers and corresp. cascade mode */
set_counter(0, value & 0x0ffff);
tmpval=inl(iocard_base+0x1c) & ~0x0400; /* T0_T2 bit isolation */
if (value & 0xffff0000) {
set_counter(2,(value>>16));
tmpval |= 0x0400; /* set T0_T2 cascade enable bit */
};
outl(tmpval,iocard_base+0x1c);
break;
case NUDAQ_2_INMODE:
return setinmode(value);
break;
/* for debugging: */
case 0x2001:
/* write to buffer adr mit offset, return kernel adr */
tmp=dma_main_pointer->buffer;
tmp[(value>>8)&0xff]=(value & 0xff);
return (unsigned int)tmp[(value>>8)&0xff];
break;
case 0x2002:
/* read buffer mot offset */
tmp=dma_main_pointer->buffer;
val=tmp[(value>>8)&0xff];
return (unsigned int)val;
break;
case 0x2003:
return (int)value;
break;
case 0x2004:
/* set adr register */
adr2 = value;
return 0;
break;
case 0x2005:
/* re-read adr register */
return (int) adr2;
break;
case 0x2006:case 0x2008:
/* set register in adr space 1 directly */
w4=value;adr=(adr2 & 0x3c)+(cmd==0x2006?iocard_base:dma_engine_base);
outl(w4,adr);
break;
case 0x2007:case 0x2009:
/* read register in adr space 1 directly */
adr=(adr2 & 0x3c)+(cmd==0x2007?iocard_base:dma_engine_base);
return (int)inl(adr);
break;
case 0x200a:
/* read bus master control status reg */
return (int) inl(dma_engine_base+0x3c);
break;
case 0x200b:
/* read interrupt control register */
return (int) inl(dma_engine_base+0x38);
break;
case 0x200c:
/* read saved value diovalsave */
return (int)diovalsave;
break;
case 0x200d:
/* read MWTC register */
return (int)inl(dma_engine_base+0x28);
break;
default:
return -EINVAL;
};
int main(int argc, char **argv)
{
double *V;
double *xx;
double *iscase;
double *iscasecorr;
int K;
int k,m,n;
int nignore;
double rowsum, rowsum1;
double chisq, Echisq, gamma, denom;
readcommands(argc, argv) ;
if (outputname != NULL)
openit(outputname, &fpout, "w") ;
else
fpout = stdout;
fprintf(fpout, "Chisq EIGENSTRAT\n");
setinmode(&inmode, imode);
packmode = YES;
numsnps =
getsnps(snpname, &snpmarkers, 0.0, NULL, &nignore, 1) ;
NSAMPLES = getindivs(indivname, &indivmarkers) ;
setstatus(indivmarkers, NSAMPLES, "Case") ;
setgenotypename(&genotypename, indivname) ;
if (genotypename != NULL) {
getgenos(genotypename, snpmarkers, indivmarkers,
numsnps, NSAMPLES, nignore) ;
}
/*******************************************************************/
/* Free memory: Usually this is done in outfiles: */
/* */
/* nind = rmindivs(&snpmarkers, numsnps, &indmarkers, NSAMPLES); */
/* */
/* But where is the snpmarkers array released? */
/*******************************************************************/
L = numpc;
readpcafile(&V, &outlier, &K, L, NSAMPLES);
getphenos(NSAMPLES, &iscase, outlier, &iscasecorr, L, V);
/* main eigenstrat loop here */
if ((xx = (double *)malloc(NSAMPLES*sizeof(*xx))) == NULL)
{ fprintf(stderr,"CM\n"); exit(1); }
for(m=0;m<numsnps;m++) {
SNP *cupt = snpmarkers[m];
for(n=0; n<NSAMPLES; n++)
{
int j = getgtypes(cupt,n);
if(j == 0) { xx[n] = 0.0; }
else if(j == 1) { xx[n] = 0.5; }
else if(j == 2 ) { xx[n] = 1.0; }
else if(j == -1) { xx[n] = -100.0; }
if(outlier[n] == 1) xx[n] = -100.0;
}
/* mean-adjust xx */
rowsum = 0.0; rowsum1 = 0.0;
for(n=0; n<NSAMPLES; n++)
{
if(qtmode == NO && ((outlier[n]) || (xx[n] < -99.0))) continue;
if(qtmode == YES && ((outlier[n]) || (xx[n] == -100.0))) continue;
rowsum += xx[n];
rowsum1 += 1.0;
}
for(n=0; n<NSAMPLES; n++)
{
if(outlier[n]) continue;
if(qtmode == NO) {
if (xx[n] < -99.0)
xx[n] = -100.0; /* still keep track */
else
xx[n] -= rowsum/rowsum1;
}
else {
if (xx[n] == -100.0)
xx[n] = -100.0; /* still keep track */
else
xx[n] -= rowsum/rowsum1;
}
}
/* Chisq */
chisq = compute_chisq(xx,iscase);
/* EIGENSTRAT */
for(k=0; k<L; k++)
{
gamma = 0.0;
denom = 0.0;
for(n=0; n<NSAMPLES; n++)
{
if(qtmode == NO && (outlier[n] || xx[n] < -99.0)) continue;
if(qtmode == YES && (outlier[n] || xx[n] == -100.0)) continue;
gamma += xx[n]*V[NSAMPLES*n+k];
denom += V[NSAMPLES*n+k]*V[NSAMPLES*n+k];
}
gamma /= denom;
for(n=0; n<NSAMPLES; n++)
{
if(qtmode == NO && (outlier[n] || xx[n] < -99.0)) continue;
if(qtmode == YES && (outlier[n] || xx[n] == -100.0)) continue;
xx[n] -= gamma*V[NSAMPLES*n+k];
}
}
Echisq = compute_chisqE(xx,iscasecorr);
if(rowsum1 == 0.0)
{
chisq = -1.0; Echisq = -1.0;
}
if(chisq >= 0.0) fprintf(fpout,"%.04f",chisq);
else fprintf(fpout,"NA");
if(Echisq >= 0.0) fprintf(fpout," %.04f\n",Echisq);
else fprintf(fpout," NA\n");
if(NSAMPLES*m > MAXSIZE)
{
fprintf(stderr,"OOPS genotype file has > %d genotypes\n",MAXSIZE);
fprintf(fpout,"OOPS genotype file has > %d genotypes\n",MAXSIZE);
exit(1);
}
}
}
