this addresses issue #10 in which some splice junctions recieve "null"

labels, which caused the enumerate function to run incorrectly.

This issue labeling junctions occured because the aligner (STAR)
assigned the read a strand flag (XS) that conflicted with the strand
implied by the sequencing protocol. 

This patch modifies IsoSCM such that splice junctions from reads with
conflicting strand information are omitted from assembled transcript
models.

IsoSCM/src/executable/IsoSCM.java

@@ -218,7 +218,7 @@ else if(jc.getParsedCommand().equals("assemble")){
 				SAMFileReader sfr = new SAMFileReader(bamFile);
 				logger.info("tabulating splice junctions...");
 				BEDWriter sj_bw = new BEDWriter(IO.bufferedPrintstream(splice_junction_bed));
-				FindSpliceJunctions.tabulateSpliceJunctions(sfr, sj_bw);
+				FindSpliceJunctions.tabulateSpliceJunctions(sfr, strandedness, sj_bw);
 				sj_bw.close();
 
 				logger.info("counting junction supporting reads...");

IsoSCM/src/processing/FindSpliceJunctions.java

@@ -114,7 +114,7 @@ public static List<AnnotatedRegion> splice_junctions(SAMRecord sr){
 		return splice_junctions;
 	}
 
-	public static StrandedGenomicIntervalTree<Map<String,Object>> tabulateSpliceJunctions(SAMFileReader sfr, BEDWriter bw){
+	public static StrandedGenomicIntervalTree<Map<String,Object>> tabulateSpliceJunctions(SAMFileReader sfr, Strandedness strandedness, BEDWriter bw){
 		Map<String,Integer> referenceLengths = BAMTools.referenceSequenceLengths(sfr.getFileHeader());
 
 		StrandedGenomicIntervalTree<Map<String,Object>> splice_junctions = new StrandedGenomicIntervalTree<Map<String,Object>>();
@@ -130,6 +130,9 @@ public static StrandedGenomicIntervalTree<Map<String,Object>> tabulateSpliceJunc
 				SAMRecord sr = sri.next();
 				if(sr.getCigarString().indexOf('N') == -1)
 					continue;
+
+				if(strandedness!=Strandedness.unstranded && sr.getAttribute("XS")!=null && BAMTools.strand(sr, strandedness)!=sr.getCharacterAttribute("XS"))
+					continue;
 
 				Cigar cigar = sr.getCigar();
 				int alignmentPosition = sr.getAlignmentStart();
@@ -869,6 +872,9 @@ public MapCounter<Integer> instantiate(Object... objects) {
 			String chr = sr.getReferenceName();
 			int alignment_start = sr.getAlignmentStart();
 
+			if(strandedness!=Strandedness.unstranded && sr.getAttribute("XS")!=null && BAMTools.strand(sr, strandedness)!=sr.getCharacterAttribute("XS"))
+				continue;
+
 			if(prev_chr!=null && !chr.equals(prev_chr)){
 				writeAll(strand_count_5p_splice,strand_count_5p_span, prev_chr, true,gw);
 				// IMPORTANT: corrected error when last read aligned to the chromosome is spliced