Update edit dist with STAR's nM tag.

mozack · Sep 15, 2017 · 430f26e · 430f26e
1 parent 6207cd5
commit 430f26e
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/src/main/java/abra/ReAligner.java b/src/main/java/abra/ReAligner.java
@@ -624,8 +624,13 @@ private void remapRead(ReadEvaluator readEvaluator, SAMRecord read, int origEdit
 					// Original edit distance
 					read.setAttribute("YX",  origEditDist);
 
+					String distTag = "NM";
+					if (orig.getAttribute("NM") == null && orig.getAttribute("nM") != null) {
+						distTag = "nM";
+					}
+
 					// Updated edit distance
-					read.setAttribute("NM", SAMRecordUtils.getEditDistance(read, c2r, false));
+					read.setAttribute(distTag, SAMRecordUtils.getEditDistance(read, c2r, false));
 
 					//TODO: Compute mapq intelligently???
 					read.setMappingQuality(Math.min(read.getMappingQuality()+10, this.maxMapq));
@@ -648,7 +653,7 @@ private void remapRead(ReadEvaluator readEvaluator, SAMRecord read, int origEdit
 						read.setAttribute("YO", null);
 						read.setAttribute("YM", null);
 						read.setAttribute("YX", null);
-						read.setAttribute("NM", orig.getAttribute("NM"));
+						read.setAttribute(distTag, orig.getAttribute(distTag));
 						read.setMappingQuality(orig.getMappingQuality());
 						read.setReadUnmappedFlag(orig.getReadUnmappedFlag());
 					}