made another change relating to a case that cropped STAR alignments

resulting in "null" junction labeling. 

The logic for defining exon boundaries assumed that the introns implied
by spliced reads will be longer than 1nt. Apparently read alignments are
sometimes reported with 1nt introns (cigar code 1N). While this doesn't
make much sense ( a 1D to represent a deletion from the reference would
be more appropriate) IsoSCM delegates to the aligner to identify intron
boundaries, and now will correctly incorporate these as 1nt introns in
the gene model.

IsoSCM/src/processing/ClusterExpressedSegments.java

@@ -345,7 +345,8 @@ public static void identifySplicedExons(File acc_jnct_gtf, File segment_bed, GTF
 			StrandedGenomicIntervalTree<Map<String,Object>> written = new StrandedGenomicIntervalTree<Map<String,Object>>();
 
 			for(AnnotatedRegion splice5p : splice5ps.overlappingRegions(r.chr, r.start-1, r.end+1, r.strand)){
-				AnnotatedRegion splice3p = splice3ps.getClosestUpstream(splice5p.chr, splice5p.start, r.strand);
+				int p = IntervalTools.offsetPosition(splice5p.start, 2, r.isNegativeStrand(), true);
+				AnnotatedRegion splice3p = splice3ps.getClosestUpstream(splice5p.chr, p, r.strand);
 				if(splice3p!=null && intervalContains(splice3p.start, r.start-1, r.end+1)){
 					while(splice3p!=null && intervalContains(splice3p.start, r.start-1, r.end+1)){
 						// write internal exon
@@ -355,7 +356,7 @@ public static void identifySplicedExons(File acc_jnct_gtf, File segment_bed, GTF
 							Map<String,Object> attributes = new HashMap<String, Object>();
 							attributes.put("type", "internal_exon");
 							// as long as there is no nested splice junction
-							if(IntervalTools.ContainedIntervals(sj, r.chr, start, end, r.strand).size()==0){
+							if(IntervalTools.ContainedIntervals(sj, r.chr, start+1, end-1, r.strand).size()==0){
 								written.add(r.chr, start+1, end-1, r.strand);
 								exons.write("exon", r.chr, start+1, end-1, r.strand,AnnotatedRegion.GTFAttributeString(attributes));
 							}
@@ -380,7 +381,8 @@ public static void identifySplicedExons(File acc_jnct_gtf, File segment_bed, GTF
 			}
 
 			for(AnnotatedRegion splice3p : splice3ps.overlappingRegions(r.chr, r.start-1, r.end+1, r.strand)){
-				AnnotatedRegion splice5p = splice5ps.getClosestDownstream(splice3p.chr, splice3p.start, r.strand);
+				int p = IntervalTools.offsetPosition(splice3p.start, 2, r.isNegativeStrand(), false);
+				AnnotatedRegion splice5p = splice5ps.getClosestDownstream(splice3p.chr, p, r.strand);
 				if(splice5p!=null && intervalContains(splice5p.start, r.start-1, r.end+1)){
 					while(splice5p!=null && intervalContains(splice5p.start, r.start-1, r.end+1)){
 						// write internal exon
@@ -390,7 +392,7 @@ public static void identifySplicedExons(File acc_jnct_gtf, File segment_bed, GTF
 							Map<String,Object> attributes = new HashMap<String, Object>();
 							attributes.put("type", "internal_exon");
 							// as long as there is no nested splice junction
-							if(IntervalTools.ContainedIntervals(sj, r.chr, start, end, r.strand).size()==0){
+							if(IntervalTools.ContainedIntervals(sj, r.chr, start+1, end-1, r.strand).size()==0){
 								written.add(r.chr, start+1, end-1, r.strand);
 								exons.write("exon", r.chr, start+1, end-1, r.strand, AnnotatedRegion.GTFAttributeString(attributes));
 							}