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/* Output from p2c, the Pascal-to-C translator */
/* From input file "linkmap.p" */
/* This file contains part of a modified version of the LINKMAP program */
/* The modifications are described in the papers: */
/* R. W. Cottingham, Jr., R. M. Idury, and A. A. Schaffer, */
/* Faster Sequential Genetic Linkage Computations */
/* American Journal of Human Genetics, 53(1993), pp. 252-263 */
/* and A. A. Schaffer, S. K. Gupta, K. Shriram, and R. W. Cottingham, Jr. */
/* Avoiding Recomputation in Genetic Linkage Analysis, */
/* Human Heredity 44(1994), pp. 225-237 */
#include "commondefs.h"
#include "gemdefs.h"
#include "lidefs.h"
Void readloci(LINK)
struct LOC_inputdata *LINK;
{
struct LOC_readloci V;
long i, j, coupling, autosomal, independent, difference;
locusvalues *WITH;
V.LINK = LINK;
lastpriv = 0;
fscanf(datafile, "%d%d%ld%*[^\n]", &mlocus, &risksys, &autosomal);
getc(datafile);
/*Replace the above line with the next when using epistasis*/
/*readln(datafile,mlocus,risksys,autosomal,lastpriv);*/
if (mlocus > maxlocus)
inputerror(0L, mlocus, mlocus, LINK);
if (mlocus <= 0)
inputerror(1L, mlocus, mlocus, LINK);
if (risksys > maxlocus)
inputerror(37L, risksys, risksys, LINK);
if (risksys < 0)
inputerror(38L, risksys, risksys, LINK);
risk = (risksys != 0);
sexlink = (autosomal == 1);
#if PARALLEL
if (Tmk_proc_id == 0) {
#endif
printf("YOU ARE USING LINKAGE (V%3.1f (1-Feb-1991)) WITH%3d-POINT\n",
fVersion, mlocus);
printf("YOU ARE USING FASTLINK (V%s (6-Oct-1997))",
fastversion);
if (sexlink)
printf(" SEXLINKED DATA\n");
else
printf(" AUTOSOMAL DATA\n");
#if PARALLEL
}
#endif
fscanf(datafile, "%d%lf%lf%ld%*[^\n]", &mutsys, &mutmale, &mutfemale,
&coupling);
getc(datafile);
if (mutsys > maxlocus)
inputerror(39L, mutsys, mutsys, LINK);
if (mutsys < 0)
inputerror(40L, mutsys, mutsys, LINK);
if (coupling == 1)
disequi = true;
else
disequi = false;
if (disequi) {
hapfreq = (thisarray *)Malloc(sizeof(thisarray));
if (!(hapfreq))
malloc_err("hapfreq");
}
for (i = 1; i <= mlocus; i++) {
fscanf(datafile, "%ld", &j);
if (j > mlocus)
inputerror(2L, i, j, LINK);
if (j <= 0)
inputerror(3L, i, j, LINK);
order[j - 1] = i;
}
for (i = 1; i <= mlocus; i++) {
for (j = 1; j < i; j++) {
if (order[i - 1] == order[j - 1])
inputerror(4L, i, j, LINK);
}
}
fscanf(datafile, "%*[^\n]");
getc(datafile);
if (mutsys != 0)
mutsys = order[mutsys - 1];
if (risksys != 0)
risksys = order[risksys - 1];
V.nupriv = 0;
for (i = 0; i < mlocus; i++)
getlocus(order[i], &V);
increment[mlocus - 1] = 1;
for (i = mlocus - 1; i >= 1; i--)
increment[i - 1] = increment[i] * thislocus[i]->nallele;
fgeno = 1;
for (j = 0; j < mlocus; j++)
fgeno *= thislocus[j]->nallele;
mgeno = fgeno;
nuhap = fgeno;
for (i = 0; i < mlocus; i++)
nohom[i] = false;
if (disequi) {
allocate_thisarray(hapfreq, mgeno);
for (i = 0; i < mgeno; i++)
fscanf(datafile, "%lf", &hapfreq->genarray[i]);
fscanf(datafile, "%*[^\n]");
getc(datafile);
} else {
for (i = 0; i < mlocus; i++) {
WITH = thislocus[i];
if (WITH->which == affection || WITH->which == quantitative) {
if (WITH->freq[affall - 1] < minfreq)
nohom[i] = true;
}
}
}
fgeno = fgeno * (fgeno + 1) / 2;
if (!sexlink)
mgeno = fgeno;
fscanf(datafile, "%ld", &difference);
if ((unsigned long)difference > 2) {
inputwarning(0L, difference, difference, LINK);
difference = 0;
}
sexdif = (difference != 0);
readfemale = (difference == 2);
fscanf(datafile, "%ld%*[^\n]", &independent);
getc(datafile);
if ((unsigned long)independent > 2) {
inputwarning(1L, independent, independent, LINK);
independent = 0;
}
interfer = (independent != 0);
mapping = (independent == 2);
gettheta(&maletheta, &V);
if (sexdif)
gettheta(&femaletheta, &V);
else
femaletheta = maletheta;
if (sexlink && sexdif) {
inputwarning(2L, difference, difference, LINK);
sexdif = false;
readfemale = false;
}
fscanf(datafile, "%d%lf%d%*[^\n]", &whichvary, &finaltheta, &gridsize);
getc(datafile);
/*Transform whichvary to chromosome order*/
whichvary = order[whichvary - 1];
if (!sexlink) {
if (mutsys == 0)
thispath = auto_;
else
thispath = mauto;
} else if (mutsys == 0)
thispath = sex;
else
thispath = msex;
segscale = scale;
for (i = 1; i <= mlocus; i++)
segscale *= scalemult;
}
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