Fixes tricky NPE in assembleContigs.

CHANGELOG_CURRENT

@@ -0,0 +1 @@
+Fixes `NPE` in very rare cases with incompatible V gene selection for `assembleContigs` in case of partially annotated gene libraries

src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java

@@ -136,10 +136,10 @@ public FullSeqAssembler(CloneFactory cloneFactory,
         this.alignerParameters = alignerParameters;
         GeneFeature[] assemblingFeatures = clone.getParentCloneSet().getAssemblingFeatures();
         if (assemblingFeatures.length != 1)
-            throw new IllegalArgumentException();
+            throw new IllegalArgumentException("Supports only singular assemblingFeature.");
 
         if (assemblingFeatures[0].isComposite())
-            throw new IllegalArgumentException();
+            throw new IllegalArgumentException("Supports only non-composite gene features as an assemblingFeature.");
 
         this.assemblingFeature = assemblingFeatures[0];
         this.genes = new VDJCGenes(baseVHit.getGene(), null, baseJHit.getGene(), null); // clone.getBestHitGenes();
@@ -1747,4 +1747,18 @@ else if (right == -1)
     private boolean inSplitRegion(int p) {
         return splitRegion != null && splitRegion.contains(p);
     }
+
+    /**
+     * Check that the V/J gene can be used for full sequence assembly algorithm. Basically it checks that is has required reference points defined.
+     *
+     * @param hit               hit to check
+     * @param assemblingFeature clonal assembling feature
+     * @return true if gene is compatible
+     */
+    public static boolean checkGeneCompatibility(VDJCHit hit, GeneFeature assemblingFeature) {
+        GeneFeature vFeature = hit.getAlignedFeature();
+        VDJCGene gene = hit.getGene();
+        GeneFeature targetFeature = GeneFeature.intersection(assemblingFeature, vFeature);
+        return gene.getPartitioning().isAvailable(targetFeature);
+    }
 }

src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java

@@ -146,12 +146,14 @@ public void run1() throws Exception {
                             .collect(Collectors.toMap(
                                     Map.Entry::getKey,
                                     e ->
-                                            Arrays.stream(e.getValue()).collect(
-                                                    Collectors.toMap(
-                                                            h -> h.getGene().getId(),
-                                                            CoverageAccumulator::new
-                                                    )
-                                            ),
+                                            Arrays.stream(e.getValue())
+                                                    .filter(h -> FullSeqAssembler.checkGeneCompatibility(h, cloneAssemblerParameters.getAssemblingFeatures()[0]))
+                                                    .collect(
+                                                            Collectors.toMap(
+                                                                    h -> h.getGene().getId(),
+                                                                    CoverageAccumulator::new
+                                                            )
+                                                    ),
                                     noMerge(),
                                     () -> new EnumMap<>(GeneType.class)));