int main (int argc, char *argv[])
{
char lineBuf[MAXLINE];
char refName[40], refb, alignString[10000], qualityString[10000];
int pos, totDepth;
int i;
FILE *plfid;
if (argc == 1) {
fprintf(stderr, "Usage: pileup2dc [in.pileup]\n");
return 1;
}
// open the pileup file for reading
// die if error opening or reading file
plfid = fopen(argv[1], "rd");
// get the number of positions in the pileup
int numLines = get_filelength(plfid);
// allocate space for the depth chart
pile_t pile[numLines];
// read the pileup file and store in the structure
for (i=0; i<numLines; i++) {
fgets(lineBuf, MAXLINE, plfid);
sscanf(lineBuf, "%s\t%d\t%c\t%d\t%s\t%s", refName, &pos, &refb,
&totDepth, alignString, qualityString);
pile[i].pos = pos;
parse_align_string ( toupper(refb), alignString, &pile[i] );
}
fclose(plfid);
// export the pileup structure in depth chart format
export_depthchart ( pile, numLines);
return 0;
}
void filter_calcs(void) {
//External variables
extern char filtersinput[FILEPATH_LENGTH];
extern char galssedinput[FILEPATH_LENGTH];
extern char starssedinput[FILEPATH_LENGTH];
//Internal variables
long *N,ii;
long sedlength = 0;
long regridfactor;
long filterlength[Nfilter];
double *pnorm;
double *filtlamb,*filtthru;
//Allocate temporary variables
N = (long *)malloc(sizeof(long));
pnorm = (double *)malloc(sizeof(double));
//How many filters?
get_num_files(filtersinput, N);
Nfilter = *N;
if (Nfilter<2) {
printf("Need more than 1 filter\n");
return;
}
printf("\n\nFound %ld Filters\n",Nfilter);
//Read in the number of star/galaxy SEDs
get_num_files(starssedinput, N);
Nstartemplate = *N;
get_num_files(galssedinput, N);
Ngaltemplate = *N;
//Find the finest SED amongst the bunch
for (ii=0;ii<Nstartemplate;ii++) {
get_filelength(ii,starssedinput,N);
if (*N * 2 > sedlength)
sedlength = *N * 2;
}
for (ii=0;ii<Ngaltemplate;ii++) {
get_filelength(ii,galssedinput,N);
if (*N * 2 > sedlength)
sedlength = *N * 2;
}
//Allocate final filter arrays, which are globals
filter_lgth_fine = (long *)malloc(Nfilter*sizeof(long));
filter_lamb_fine = malloc(Nfilter*sizeof(double*));
filter_thru_fine = malloc(Nfilter*sizeof(double*));
norm = (double *)malloc(Nfilter*sizeof(double));
//Loop over the filters in the file
for (ii=0;ii<Nfilter;ii++) {
//get length
get_filelength(ii,filtersinput, N);
filterlength[ii] = *N;
regridfactor = round((float)sedlength / (float)*N);
filter_lgth_fine[ii] = *N * regridfactor;
//alloc filter arrays
filtlamb = (double *)malloc(*N * sizeof(double));
filtthru = (double *)malloc(*N * sizeof(double));
filter_lamb_fine[ii] = (double *)malloc(regridfactor * *N * sizeof(double));
filter_thru_fine[ii] = (double *)malloc(regridfactor * *N * sizeof(double));
//read in the 2 column ascii filter file
read_file(ii,filtersinput,filtlamb,filtthru);
//regrid the filter to user spec, using gsl spline interpolation
regrid_filter(filtlamb,filtthru,filterlength[ii],filter_lgth_fine[ii], \
filter_lamb_fine[ii],filter_thru_fine[ii]);
//calculate the flux zeropoint
calc_normalization(filter_lamb_fine[ii],filter_thru_fine[ii], \
filter_lgth_fine[ii],pnorm);
norm[ii] = *pnorm;
printf("Filter %ld has (AB) zeropoint flux normalization: %g\n",ii,norm[ii]);
free(filtlamb);
free(filtthru);
}
free(pnorm);
free(N);
}
