std::string QtUtils::GetOpenFileName(
const std::string &filter,
const std::string &caption,
const std::string &dir)
{
QString qcaption(caption.c_str());
QString qdir(dir.c_str());
QString qfilter(filter.c_str());
QWidget *parent = 0;
QString filename = QFileDialog::getOpenFileName(parent, qcaption, qdir, qfilter);
return filename.toStdString();
}
QStringList QtUtils::GetOpenRexFilenames(const std::string &dir)
{
QString qfilter(
"Images (*.tga; *.bmp; *.jpg; *.jpeg; *.png);;"
"Sounds (*.ogg; *.wav);;"
"Ogre 3D Models (*.mesh);;"
"Ogre Particle Scripts (*.particle);;"
"Ogre Skeleton (*.skeleton);;"
"Ogre Material (*.material);;"
"Flash Animation (*.swf);;"
"All Files (*.*)");
QString qcaption("Open");
QString qdir(dir.c_str());
QWidget *parent = 0;
return QFileDialog::getOpenFileNames(parent, qcaption, qdir, qfilter);
}
StringList QtUtils::GetOpenFileNames(
const std::string &filter,
const std::string &caption,
const std::string &dir)
{
QString qcaption(caption.c_str());
QString qdir(dir.c_str());
QString qfilter(filter.c_str());
QWidget *parent = 0;
StringList filelist;
QStringList filenames = QFileDialog::getOpenFileNames(parent, qcaption, qdir, qfilter);
// Convert QStringList to std::list<std::string> list.
for(QStringList::iterator q_it = filenames.begin(); q_it != filenames.end(); ++q_it)
filelist.push_back(q_it->toStdString());
return filelist;
}
StringList QtUtils::GetOpenRexFileNames(const std::string &dir)
{
QString qfilter(
"Images (*.tga; *.bmp; *.jpg; *.jpeg; *.png);;"
"Sounds (*.ogg; *.wav);;"
"Ogre 3D Models (*.mesh);;"
"Ogre Particle Scripts (*.particle);;"
"Ogre Skeleton (*.skeleton);;"
"Ogre Material (*.material);;"
"Flash Animation (*.swf);;"
"All Files (*.*)");
QString qcaption("Open");
QString qdir(dir.c_str());
QWidget *parent = 0;
StringList filelist;
QStringList filenames = QFileDialog::getOpenFileNames(parent, qcaption, qdir, qfilter);
// Convert QStringList to std::list<std::string> list.
for(QStringList::iterator q_it = filenames.begin(); q_it != filenames.end(); ++q_it)
filelist.push_back(q_it->toStdString());
return filelist;
}
int make_ld(unsigned int tid, unsigned int pos, int n, const bam_pileup1_t *pl, void *data)
{
int i;
int fq;
unsigned long long sample_cov;
unsigned long long *cb = NULL;
ldData *t = NULL;
// get control data structure
t = (ldData*)data;
// only consider sites located in designated region
if ((t->beg <= (int)pos) && (t->end > (int)pos))
{
// allocate memory pileup data
try
{
cb = new unsigned long long [t->sm->n]();
}
catch (std::bad_alloc& ba)
{
std::cerr << "bad_alloc caught: " << ba.what() << std::endl;
}
// call bases
t->call_base(n, pl, cb);
// resolve heterozygous sites
if (!(t->flag & BAM_HETEROZYGOTE))
clean_heterozygotes(t->sm->n, cb, (int)t->ref_base[pos], t->min_snpQ);
// determine if site is segregating
fq = segbase(t->sm->n, cb, t->ref_base[pos], t->min_snpQ);
// determine how many samples pass the quality filters
sample_cov = qfilter(t->sm->n, cb, t->min_rmsQ, t->min_depth, t->max_depth);
for (i=0; i < t->sm->npops; i++)
t->pop_sample_mask[i] = sample_cov & t->pop_mask[i];
if (popcount64(sample_cov) == t->sm->n)
{
// calculate the site type
t->types[t->num_sites] = t->cal_site_type(cb);
if (fq > 0)
{
t->hap.pos[t->segsites] = pos;
t->hap.ref[t->segsites] = bam_nt16_table[(int)t->ref_base[pos]];
for (i=0; i < t->sm->n; i++)
{
t->hap.rms[i][t->segsites] = (cb[i]>>(CHAR_BIT*6))&0xffff;
t->hap.snpq[i][t->segsites] = (cb[i]>>(CHAR_BIT*4))&0xffff;
t->hap.num_reads[i][t->segsites] = (cb[i]>>(CHAR_BIT*2))&0xffff;
t->hap.base[i][t->segsites] = bam_nt16_table[(int)iupac[(cb[i]>>CHAR_BIT)&0xff]];
if (cb[i]&0x2ULL)
t->hap.seq[i][t->segsites/64] |= 0x1ULL << t->segsites%64;
}
t->hap.idx[t->segsites] = t->num_sites;
t->segsites++;
}
t->num_sites++;
}
