static void
print_flist_1(
flist_t *flist,
char **ppfx,
int parentoff)
{
char buf[16];
const field_t *f;
const ftattr_t *fa;
flist_t *fl;
int low;
int neednl;
char **pfx;
for (fl = flist; fl && !seenint(); fl = fl->sibling) {
pfx = copy_strvec(ppfx);
if (fl->name[0])
add_strvec(&pfx, fl->name);
if (fl->flags & FL_OKLOW) {
add_strvec(&pfx, "[");
snprintf(buf, sizeof(buf), "%d", fl->low);
add_strvec(&pfx, buf);
if (fl->low != fl->high) {
add_strvec(&pfx, "-");
snprintf(buf, sizeof(buf), "%d", fl->high);
add_strvec(&pfx, buf);
}
add_strvec(&pfx, "]");
}
if (fl->child) {
if (fl->name[0])
add_strvec(&pfx, ".");
print_flist_1(fl->child, pfx, fl->offset);
} else {
f = fl->fld;
fa = &ftattrtab[f->ftyp];
ASSERT(fa->ftyp == f->ftyp);
print_strvec(pfx);
dbprintf(" = ");
if (fl->flags & FL_OKLOW)
low = fl->low;
else
low = 0;
if (fa->prfunc) {
neednl = fa->prfunc(iocur_top->data, fl->offset,
fcount(f, iocur_top->data, parentoff),
fa->fmtstr,
fsize(f, iocur_top->data, parentoff, 0),
fa->arg, low,
(f->flags & FLD_ARRAY) != 0);
if (neednl)
dbprintf("\n");
} else {
ASSERT(fa->arg & FTARG_OKEMPTY);
dbprintf(_("(empty)\n"));
}
}
free_strvec(pfx);
}
}
int main (int argc, char** argv){
double timing = get_time();
double start_time = timing;
Parameter myPara (argc, argv);
GlobalParam gParam;
// -------------------------------------------------------------------
//std::cout << "Get input bam file list...\n\n";
//xny::getInputFilelist (gParam.bam_filelist, "bam", myPara.iDirNm);
gParam.bam_filelist.push_back(myPara.iDirNm);
if (gParam.bam_filelist.size() == 0) abording ("no .bam file found");
else {
int sz = gParam.bam_filelist.size();
std::cout << "\n\t" << sz << " bam file(s) found: \n";
print_strvec ("\t\t", gParam.bam_filelist);
}
// -------------------------------------------------------------------
std::cout << "\nParse bam header: get refSeq info & sanity check\n\n";
parse_bam_header (gParam, myPara.pSample);
// -------------------------------------------------------------------
std::cout << "\nGet maxQ, minQ, maxReadLen, avgFragSz, "
"stdFragSz from bam files ...\n\n";
int min_qual, max_qual;
sampling (min_qual, max_qual, gParam.maxRL, gParam.avgFragSz,
gParam.stdFragSz, gParam.bam_filelist, myPara.pSample);
if (max_qual - min_qual + 1 < myPara.var_qt) {
myPara.var_qt = max_qual - min_qual + 1;
std::cout << "\tqQuantile is reset to " << myPara.var_qt << "\n";
}
// -------------------------------------------------------------------
std::cout << "\nGenerate qual -> quantile map ... \n\n";
qqMap (gParam.qq, min_qual, max_qual, myPara.var_qt);
// -------------------------------------------------------------------
std::cout << "\nSet up paired read map arrays ... \n\n";
set_rmap_array (gParam, myPara);
//set_arrays (gParam, qq, myPara);
// remeasure fragment size based on paired read alignment as the
// BAM file did not properly record such information
if (gParam.avgFragSz == 0) {
ivec_t fragSz;
std::map<std::string, MapEntry>::iterator it_am = gParam.alnMap.begin();
for (; it_am != gParam.alnMap.end(); ++ it_am) {
if (it_am->second.second.start >= it_am->second.first.start){
fragSz.push_back(it_am->second.second.start -
it_am->second.first.start);
}
}
/* calculate mean frag sz and std */
int sample_sz = fragSz.size();
uint64_t sum = 0;
for (int i = 0; i < sample_sz; ++ i) sum += fragSz[i];
if (sum > 0 && sample_sz > 0) gParam.avgFragSz = sum/sample_sz;
sum = 0;
for (int i = 0; i < (int) fragSz.size(); ++ i) {
sum += (gParam.avgFragSz - fragSz[i])*(gParam.avgFragSz - fragSz[i]);
}
if (sample_sz > 1) gParam.stdFragSz = std::sqrt(sum/sample_sz - 1);
std::cout << "\trecalculated frag size and std" << gParam.avgFragSz
<< ", " << gParam.stdFragSz << "\n";
}
// -------------------------------------------------------------------
std::cout << "\nPrepare aln columns file...\n\n";
prep_aln_file (gParam, myPara);
// -------------------------------------------------------------------
std::cout << "\nInference ...\n\n";
EM (gParam, myPara);
std::cout << "-----------------------------------------------------------\n\n";
print_time("Whole program takes \t", start_time);
std::cout << "DONE!\n";
return (EXIT_SUCCESS);
}
