//err_dep = 0.83
void bam_likes_init(){
mod = errmod_init(1-ERR_DEP);
}
int main_ld(int argc, char *argv[])
{
int chr; //! chromosome identifier
int beg; //! beginning coordinate for analysis
int end; //! end coordinate for analysis
int ref; //! ref
long num_windows; //! number of windows
std::string msg; //! string for error message
bam_plbuf_t *buf; //! pileup buffer
ldData t;
// parse the command line options
std::string region = t.parseCommandLine(argc, argv);
// check input BAM file for errors
t.checkBAM();
// initialize the sample data structure
t.bam_smpl_init();
// add samples
t.bam_smpl_add();
// initialize error model
t.em = errmod_init(1.0-0.83);
// parse genomic region
int k = bam_parse_region(t.h, region, &chr, &beg, &end);
if (k < 0)
{
msg = "Bad genome coordinates: " + region;
fatal_error(msg, __FILE__, __LINE__, 0);
}
// fetch reference sequence
t.ref_base = faidx_fetch_seq(t.fai_file, t.h->target_name[chr], 0, 0x7fffffff, &(t.len));
// calculate the number of windows
if (t.flag & BAM_WINDOW)
num_windows = ((end-beg)-1)/t.win_size;
else
{
t.win_size = (end-beg);
num_windows = 1;
}
// iterate through all windows along specified genomic region
for (long cw=0; cw < num_windows; cw++)
{
// construct genome coordinate string
std::string scaffold_name(t.h->target_name[chr]);
std::ostringstream winc(scaffold_name);
winc.seekp(0, std::ios::end);
winc << ":" << beg+(cw*t.win_size)+1 << "-" << ((cw+1)*t.win_size)+(beg-1);
std::string winCoord = winc.str();
// initialize number of sites to zero
t.num_sites = 0;
// parse the BAM file and check if region is retrieved from the reference
if (t.flag & BAM_WINDOW)
{
k = bam_parse_region(t.h, winCoord, &ref, &(t.beg), &(t.end));
if (k < 0)
{
msg = "Bad window coordinates " + winCoord;
fatal_error(msg, __FILE__, __LINE__, 0);
}
}
else
{
ref = chr;
t.beg = beg;
t.end = end;
if (ref < 0)
{
msg = "Bad scaffold name: " + region;
fatal_error(msg, __FILE__, __LINE__, 0);
}
}
// initialize nucdiv variables
t.init_ld();
// create population assignments
t.assign_pops();
// initialize pileup
buf = bam_plbuf_init(make_ld, &t);
// fetch region from bam file
if ((bam_fetch(t.bam_in->x.bam, t.idx, ref, t.beg, t.end, buf, fetch_func)) < 0)
{
msg = "Failed to retrieve region " + region + " due to corrupted BAM index file";
fatal_error(msg, __FILE__, __LINE__, 0);
}
// finalize pileup
bam_plbuf_push(0, buf);
// calculate linkage disequilibrium statistics
ld_func fp[3] = {&ldData::calc_zns, &ldData::calc_omegamax, &ldData::calc_wall};
(t.*fp[t.output])();
// print results to stdout
t.print_ld(chr);
// take out the garbage
t.destroy_ld();
bam_plbuf_destroy(buf);
}
// end of window interation
errmod_destroy(t.em);
samclose(t.bam_in);
bam_index_destroy(t.idx);
t.bam_smpl_destroy();
free(t.ref_base);
return 0;
}