Log when leading insert encountered in contig alignment.

mozack · Sep 21, 2018 · a905187 · a905187
1 parent 605b118
commit a905187
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/src/main/java/abra/ContigAligner.java b/src/main/java/abra/ContigAligner.java
@@ -77,6 +77,10 @@ public ContigAlignerResult align(String seq) {
 
 			CigarElement first = cigar.getFirstCigarElement();
 			CigarElement last = cigar.getLastCigarElement();
+
+			if (first.getOperator() == CigarOperator.I) {
+				Logger.trace("Contig with leading insert: [%s] - [%s]", sgResult, seq);
+			}
 
 			// Do not allow indels at the edges of contigs.
 			if (minAnchorLength > 0 &&