Potential Bug Related to Exonic Breakpoints

[thomas-coard-nih]

While using Pegasus, I think that I encountered a bug relating to exonic breakpoints. Currently if a breakpoint is in an exon, it will not enter the if statement block on line 1612 because the breakpoint position will not be greater than that exon’s end position. This causes none of that exon’s coordinates to be returned, making the previous exon the last exon whose data is returned.

Line 1612 could likely be fixed by replacing “l.end()” with “l.start()”. It is possible that there are similar errors elsewhere in the code.

In my limited testing, this bug only pertains to exonic breakpoints and not intronic breakpoints.

source/java_modules/FusionSequenceFromGTF/src/FusionSequenceFromGTF/FusionSequenceFrom

Pegasus/source/java_modules/FusionSequenceFromGTF/src/FusionSequenceFromGTF/FusionSequenceFromGTF.java

Lines 1606 to 1636 in f37b564

	//5' positive strand
	if(fiveprimegene.getGeneStrand().compareTo("+")==0)
	{
	for (Location l : locationList)
	{
	if(l.end()<=fiveprimegene.getGeneBreakpoint())
	{
	if(l.start()<=fiveprimegene.getGeneBreakpoint() && l.end()>=fiveprimegene.getGeneBreakpoint())
	{
	lastlocation = new Location(l.start(),fiveprimegene.getGeneBreakpoint());
	overlap_breakpoint=true;
	sb.append(getSequenceStringFromLocation(
	indexedfasta,
	fiveprime_ref,
	fiveprimegene.getGeneStrand(),
	l.start()+1,
	fiveprimegene.getGeneBreakpoint()));
	}
	else
	{
	lastlocation = new Location(l);
	sb.append(getSequenceStringFromLocation(
	indexedfasta,
	fiveprime_ref,
	fiveprimegene.getGeneStrand(),
	l.start()+1,
	l.end()));
	}
	}
	}