int getMaxClipLen( SamRecord & sam_rec )
{
Cigar * myCigar = sam_rec.getCigarInfo();
int begin_clip = myCigar->getNumBeginClips();
int end_clip = myCigar->getNumEndClips();
if (begin_clip >= end_clip)
return begin_clip;
else
return -end_clip;
}
void Sites::addToCurrentCluster( vector<bool> & is_in_coord, SingleSite & new_site, SamRecord & rec )
{
if (is_in_coord.size() != NMEI)
morphError("[Sites::setNewCluster] is_in_coord size error");
// update breakpoint
int old_evi = new_site.evidence;
float a1 = (float)1 / float(old_evi+1);
int ep = getEstimatedBreakPoint(rec);
new_site.breakp = round( a1 * (float)ep + (float)new_site.breakp * (1-a1));
new_site.evidence++;
// update position
if (rec.get1BasedPosition() < new_site.start)
new_site.start = rec.get1BasedPosition();
else if (rec.get1BasedAlignmentEnd() > new_site.end)
new_site.end = rec.get1BasedAlignmentEnd();
// update info
if (rec.getFlag() & 0x10) {
if (new_site.right_clip_only) {
Cigar * myCigar = rec.getCigarInfo();
int begin_clip = myCigar->getNumBeginClips();
if ( begin_clip < MIN_CLIP/2)
new_site.right_clip_only = 0;
}
for(int m=0; m<NMEI; m++) {
if (is_in_coord[m])
new_site.right[m]++;
}
}
else {
if (new_site.left_clip_only) {
Cigar * myCigar = rec.getCigarInfo();
int end_clip = myCigar->getNumEndClips();
if (end_clip < MIN_CLIP/2)
new_site.left_clip_only = 0;
}
for( int m=0; m<NMEI; m++) {
if (is_in_coord[m])
new_site.left[m]++;
}
}
}
void Sites::setNewCluster( vector<bool> & is_in_coord, SingleSite & new_site, SamRecord & rec )
{
if (is_in_coord.size() != NMEI)
morphError("[Sites::setNewCluster] is_in_coord size error");
// set info
new_site.breakp = getEstimatedBreakPoint(rec);
new_site.rcount = 1;
new_site.evidence = 1;
for(int m=0; m<NMEI; m++) {
new_site.left[m] = 0;
new_site.right[m] = 0;
}
new_site.left_clip_only = 1;
new_site.right_clip_only = 1;
new_site.depth = current_depth;
new_site.depth_add = 1;
// set position & mtype
if ( rec.getFlag() & 0x10 ) { // right anchor
new_site.start = rec.get1BasedPosition();
new_site.end = rec.get1BasedAlignmentEnd();
Cigar * myCigar = rec.getCigarInfo();
int begin_clip = myCigar->getNumBeginClips();
if ( begin_clip < MIN_CLIP/2)
new_site.right_clip_only = 0;
for(int m=0; m<NMEI; m++) {
if (is_in_coord[m])
new_site.right[m] = 1;
}
}
else {
new_site.start = rec.get1BasedPosition();
new_site.end = rec.get1BasedAlignmentEnd();
Cigar * myCigar = rec.getCigarInfo();
int end_clip = myCigar->getNumEndClips();
if (end_clip < MIN_CLIP/2)
new_site.left_clip_only = 0;
for(int m=0; m<NMEI; m++) {
if (is_in_coord[m])
new_site.left[m] = 1;
}
}
}