Fix correct splitRegion in full seq assembler

milaboratory · Feb 12, 2018 · 67bbafa · 67bbafa
1 parent c9848ba
commit 67bbafa
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 7 deletions.
diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java
@@ -6,10 +6,8 @@
 import com.milaboratory.core.alignment.*;
 import com.milaboratory.core.mutations.MutationsBuilder;
 import com.milaboratory.core.sequence.*;
-import com.milaboratory.mixcr.basictypes.Clone;
-import com.milaboratory.mixcr.basictypes.VDJCAlignments;
-import com.milaboratory.mixcr.basictypes.VDJCHit;
-import com.milaboratory.mixcr.basictypes.VDJCPartitionedSequence;
+import com.milaboratory.mixcr.basictypes.*;
+import com.milaboratory.mixcr.cli.ActionExportClonesPretty;
 import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters;
 import gnu.trove.impl.Constants;
 import gnu.trove.iterator.TIntIntIterator;
@@ -134,11 +132,11 @@ public FullSeqAssembler(FullSeqAssemblerParameters parameters, Clone clone, VDJC
             if (parameters.subCloningRegion != null) {
                 int p = gene.getPartitioning().getRelativePosition(jFeature, parameters.subCloningRegion.getLastPoint());
                 if (p != -1)
-                    splitRegionEnd = nLeftDummies + lengthV + assemblingFeatureLength + p;
+                    splitRegionEnd = nLeftDummies + lengthV + assemblingFeatureLength - jOffset + p;
 
                 p = gene.getPartitioning().getRelativePosition(jFeature, parameters.subCloningRegion.getFirstPoint());
                 if (p != -1)
-                    splitRegionBegin = nLeftDummies + lengthV + assemblingFeatureLength + p;
+                    splitRegionBegin = nLeftDummies + lengthV + assemblingFeatureLength - jOffset + p;
             }
         } else {
             this.jOffset = 0;

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java
@@ -70,7 +70,7 @@ public void setParentCloneSet(CloneSet set) {
 
     public double getFraction() {
         if (parent == null)
-            throw new NullPointerException("Parent not set yet.");
+            return Double.NaN;
         return getFraction(parent.getTotalCount());
     }