Bug fix: count start coord in fragment length

yztxwd · yztxwd · commit 5b86aa206acd · 2025-06-26T16:54:29.000-04:00
1-based coordinates should be end - start + 1 when computing fragment
length
diff --git a/src/org/seqcode/deepseq/StrandedPair.java b/src/org/seqcode/deepseq/StrandedPair.java
@@ -52,8 +52,8 @@ public Point getMidpoint(){
 	public int getFragmentSize(){
 		if(!sameChrom)
 			return -1;
-		else if((r1Coordinate<r2Coordinate && r1Strand=='+' && r2Strand=='-') || (r2Coordinate<r1Coordinate && r2Strand=='+' && r1Strand=='-')){
-			return Math.abs(r2Coordinate-r1Coordinate);
+		else if((r1Coordinate<=r2Coordinate && r1Strand=='+' && r2Strand=='-') || (r2Coordinate<=r1Coordinate && r2Strand=='+' && r1Strand=='-')){
+			return Math.abs(r2Coordinate-r1Coordinate)+1;
 		}else{
 			return -1;
 		}
