Include spur in the set of overlaps that are isOverlapBadQuality().

huangziyan11111 · May 14, 2020 · 911fd66 · 911fd66
1 parent ed3c02f
commit 911fd66
Showing 1 changed file with 14 additions and 7 deletions.
diff --git a/src/bogart/AS_BAT_BestOverlapGraph.C b/src/bogart/AS_BAT_BestOverlapGraph.C
@@ -852,8 +852,9 @@ BestOverlapGraph::isOverlapBadQuality(BAToverlap& olap) const {
   bool   isIgnV = false;
   bool   isIgnI = false;
   bool   isBadL = false;
+  bool   isBadG = false;
+  bool   isBadS = false;
   bool   isBadO = false;
-  bool   isBadC = false;
 
   if (olap.erate() > _errorLimit)                  //  Our only real test is on
     isBadE = true;                                 //  overlap error rate.
@@ -870,9 +871,13 @@ BestOverlapGraph::isOverlapBadQuality(BAToverlap& olap) const {
       (isLopsided(olap.b_iid) == true))            //  lopsided read.
     isBadL = true;
 
-  if ((isCoverageGap(olap.a_iid) == true) ||         //  Bad if the edge touches a
-      (isCoverageGap(olap.b_iid) == true))           //  coverage-gap read.
-    isBadC = true;
+  if ((isCoverageGap(olap.a_iid) == true) ||       //  Bad if the edge touches a
+      (isCoverageGap(olap.b_iid) == true))         //  coveragegap read.
+    isBadG = true;
+
+  if ((isSpur(olap.a_iid) == true) ||              //  Bad if the edge touches a
+      (isSpur(olap.b_iid) == true))                //  spurpath read.
+    isBadS = true;
 
   if (_minOlapPercent > 0.0) {
     uint32  lenA = RI->readLength(olap.a_iid);     //  But retract goodness if the
@@ -891,7 +896,8 @@ BestOverlapGraph::isOverlapBadQuality(BAToverlap& olap) const {
                    (isIgnV == true) ||
                    (isIgnI == true) ||
                    (isBadL == true) ||
-                   (isBadC == true) ||
+                   (isBadG == true) ||
+                   (isBadS == true) ||
                    (isBadO == true));
 
   //  Now just a bunch of logging.
@@ -900,7 +906,7 @@ BestOverlapGraph::isOverlapBadQuality(BAToverlap& olap) const {
       ((olap.a_iid != 0) ||                      //  is specifically annoying (the default is to
        (olap.a_iid == 0) ||                      //  log for all reads (!= 0).
        (olap.a_iid == 0)))
-    writeLog("isOverlapBadQuality()-- %6d %6d %c  hangs %6d %6d err %.5f -- %c%c%c%c%c%c\n",
+    writeLog("isOverlapBadQuality()-- %6d %6d %c  hangs %6d %6d err %.5f -- %c%c%c%c%c%c%c\n",
              olap.a_iid, olap.b_iid,
              olap.flipped ? 'A' : 'N',
              olap.a_hang,
@@ -910,7 +916,8 @@ BestOverlapGraph::isOverlapBadQuality(BAToverlap& olap) const {
              (isIgnV) ? 't' : 'f',
              (isIgnI) ? 't' : 'f',
              (isBadL) ? 't' : 'f',
-             (isBadC) ? 't' : 'f',
+             (isBadG) ? 't' : 'f',
+             (isBadS) ? 't' : 'f',
              (isBadO) ? 't' : 'f');
 
   return(olap.filtered);