Allow partial read placements for bubbles at the edges of tigs

huangziyan11111 · May 15, 2020 · 9e1cf35 · 9e1cf35
1 parent 3430d35
commit 9e1cf35
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/src/bogart/AS_BAT_MergeOrphans.C b/src/bogart/AS_BAT_MergeOrphans.C
@@ -359,7 +359,7 @@ findOrphanReadPlacements(TigVector       &tigs,
 
     vector<overlapPlacement>   placements;
 
-    placeReadUsingOverlaps(tigs, NULL, rdA->ident, placements, placeRead_noExtend);
+    placeReadUsingOverlaps(tigs, NULL, rdA->ident, placements, allowOrphanPlacement ? placeRead_all : placeRead_noExtend);
 
     //  Weed out placements that aren't for orphans, or that are for orphans but are poor quality.  Or are to ourself!
 

diff --git a/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C b/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C
@@ -423,12 +423,16 @@ placeRead_computePlacement(overlapPlacement &op,
   op.verified.end = endVer3;
 #endif
 
-  //  Finally, limit verified to be the extent of the tig, or the extent of the placement.
+  //  Finally, limit coordinates to be the extent of the tig, or the extent of the placement.
 
   if (isFwd) {
+    if (op.position.bgn < 0)                  op.position.bgn = 0;
+    if (op.position.end > tigLen)             op.position.end = tigLen;
     if (op.verified.bgn < 0)                  op.verified.bgn = 0;
     if (op.verified.end > tigLen)             op.verified.end = tigLen;
   } else {
+    if (op.position.bgn > tigLen)             op.position.bgn = tigLen;
+    if (op.position.end < 0)                  op.position.end = 0;
     if (op.verified.bgn > tigLen)             op.verified.bgn = tigLen;
     if (op.verified.end < 0)                  op.verified.end = 0;
   }