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;
}
Exemple #2
0
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]++;
		}
	}
}
Exemple #3
0
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;
		}
	}	
}