added RC_Feature::movlcount to keep track of exon overlap lengths

gpertea · gpertea · commit 52a43d9481d9 · 2015-05-15T13:21:18.000-04:00
diff --git a/tablemaker.cpp b/tablemaker.cpp
@@ -41,10 +41,18 @@ struct COvlSorter {
   }
 } OvlSorter;
 
-void rc_updateExonCounts(const RC_Feature* exon, int nh) {
-  exon->rcount++;
-  exon->mrcount += (nh > 1) ? (1.0/nh) : 1;
-  if (nh<=1)  exon->ucount++;
+void rc_updateExonCounts(const RC_ExonOvl& exonovl, int nh) {
+  //this only gets read overlaps > 5bp and otherwise filtered in evalReadAln()
+  exonovl.feature->rcount++;
+  if (nh>1) {
+	  exonovl.feature->mrcount += (1.0/nh);
+	  exonovl.feature->movlcount += ((double)exonovl.ovlen/nh);
+  }
+  else { // nh<=1
+	  exonovl.feature->mrcount++;
+	  exonovl.feature->movlcount += exonovl.ovlen;
+	  exonovl.feature->ucount++;
+  }
 }
 
 bool BundleData::evalReadAln(GReadAlnData& alndata, char& xstrand) {
@@ -81,7 +89,7 @@ bool BundleData::evalReadAln(GReadAlnData& alndata, char& xstrand) {
 				 //      spanned by this same read alignment
 				 //counting this overlap for multiple exons if it's similarly large
 				 //(in the shared region of overlapping exons)
-				 rc_updateExonCounts(exonOverlaps[k].feature, nh);
+				 rc_updateExonCounts(exonOverlaps[k], nh);
 			 }
 		 //} //exon overlap >= 5
 	 } //ref exon overlaps
diff --git a/tablemaker.h b/tablemaker.h
@@ -58,8 +58,11 @@ struct RC_Feature { //exon or intron of a reference transcript
 	char strand;
 	mutable uint rcount; //# read alignments overlapping this feature (>5bp overlaps for exons;
 	                     // exact coord. match for introns)
-	mutable uint ucount; //# uniquely mapped reads overlapping this ref feature
-	mutable double mrcount; //multi-mapping weighted counts
+	mutable uint ucount; //# uniquely mapped reads overlapping/matching this ref feature
+	mutable double mrcount; //multi-map weighted read counts overlapping/matching this feature
+
+	mutable double movlcount; //exons only: multi-map weighted sum of overlap lengths
+
     double avg;
     double stdev;
     double mavg;
@@ -72,16 +75,16 @@ struct RC_Feature { //exon or intron of a reference transcript
 	};
 
 	RC_Feature(int l0=0, int r0=0, char s='.', uint fid=0, uint tid=0): id(fid), t_ids(1), l(l0), r(r0),
-		strand(s), rcount(0),ucount(0),mrcount(0), avg(0), stdev(0), mavg(0), mstdev(0) {
+		strand(s), rcount(0),ucount(0),mrcount(0), movlcount(0), avg(0), stdev(0), mavg(0), mstdev(0) {
 	if (l>r) { int t=l; l=r; r=t; }
 	if (tid>0) t_ids.Add(tid);
 	}
 	RC_Feature(const RC_Feature& seg): id(seg.id), t_ids(seg.t_ids), l(seg.l), r(seg.r),
-			strand(seg.strand), rcount(0),ucount(0),mrcount(0), avg(0), stdev(0), mavg(0), mstdev(0) {
+			strand(seg.strand), rcount(0),ucount(0),mrcount(0), movlcount(0), avg(0), stdev(0), mavg(0), mstdev(0) {
 	}
 
 	RC_Feature(const RC_Feature& seg, uint tid): id(seg.id), t_ids(1), l(seg.l), r(seg.r),
-		strand(seg.strand), rcount(0),ucount(0),mrcount(0), avg(0), stdev(0), mavg(0), mstdev(0) {
+		strand(seg.strand), rcount(0),ucount(0),mrcount(0), movlcount(0), avg(0), stdev(0), mavg(0), mstdev(0) {
 	if (l>r) { int t=l; l=r; r=t; }
 	if (tid>0) t_ids.Add(tid);
 	}
