Merge branch 'release/v3.0.9'

milaboratory · Aug 6, 2019 · 1bc4875 · 1bc4875
2 parents 98f1240 + 80a6afd
commit 1bc4875
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diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,14 @@
 
+MiXCR 3.0.9 ( 6 Aug 2019)
+========================
+
+-- Chain usage statistics added to `align` and `assemble` JSON reports
+-- Fixed wrong behaviour with score-based pre-filtering in `split-by-V/J=true` cases
+-- Fixed rare IndexOutOfBounds exception in `-nFeatureImputed ...`
+-- Added shortcut for `--json-report` = `-j`
+-- Sanity check for common mistake in `analyze` parameters
+
+
 MiXCR 3.0.8 (22 Jul 2019)
 ========================
 

diff --git a/pom.xml b/pom.xml
@@ -33,7 +33,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>3.0.8</version>
+    <version>3.0.9</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 

diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java
@@ -629,6 +629,7 @@ public List<CloneAccumulator> build() {
             final TIntObjectHashMap<TIntArrayList> reversePreClustered = new TIntObjectHashMap<>();
 
             Arrays.sort(accs, CLONE_ACCUMULATOR_COMPARATOR);
+            double minCountForMaxScore = accs[0].getCount() / parameters.preClusteringCountFilteringRatio;
             int deleted = 0;
 
             for (int i = 0; i < accs.length - 1; i++) {
@@ -677,10 +678,13 @@ public List<CloneAccumulator> build() {
             // Score filtering step
 
             // Calculation
+
             float[] maxScores = new float[2];
             for (CloneAccumulator acc : accs) {
                 if (acc == null)
                     continue;
+                if (acc.getCount() < minCountForMaxScore)
+                    continue;
                 for (int i = 0; i < 2; i++) {  // Only for V and J
                     GeneType gt = GeneType.VJC_REFERENCE[i];
                     maxScores[i] =

diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java
@@ -56,6 +56,7 @@ public final class CloneAssemblerParameters implements java.io.Serializable {
     boolean separateByV, separateByJ, separateByC;
     double maximalPreClusteringRatio;
     double preClusteringScoreFilteringRatio;
+    double preClusteringCountFilteringRatio;
     boolean addReadsCountOnClustering;
     byte badQualityThreshold;
     double maxBadPointsPercent;
@@ -75,6 +76,7 @@ public CloneAssemblerParameters(@JsonProperty("assemblingFeatures") GeneFeature[
                                     @JsonProperty("separateByC") boolean separateByC,
                                     @JsonProperty("maximalPreClusteringRatio") double maximalPreClusteringRatio,
                                     @JsonProperty("preClusteringScoreFilteringRatio") double preClusteringScoreFilteringRatio,
+                                    @JsonProperty("preClusteringCountFilteringRatio") double preClusteringCountFilteringRatio,
                                     @JsonProperty("addReadsCountOnClustering") boolean addReadsCountOnClustering,
                                     @JsonProperty("badQualityThreshold") byte badQualityThreshold,
                                     @JsonProperty("maxBadPointsPercent") double maxBadPointsPercent,
@@ -90,6 +92,7 @@ public CloneAssemblerParameters(@JsonProperty("assemblingFeatures") GeneFeature[
         this.separateByC = separateByC;
         this.maximalPreClusteringRatio = maximalPreClusteringRatio;
         this.preClusteringScoreFilteringRatio = preClusteringScoreFilteringRatio;
+        this.preClusteringCountFilteringRatio = preClusteringCountFilteringRatio;
         this.addReadsCountOnClustering = addReadsCountOnClustering;
         this.badQualityThreshold = badQualityThreshold;
         this.maxBadPointsPercent = maxBadPointsPercent;
@@ -264,6 +267,11 @@ public CloneAssemblerParameters setPreClusteringScoreFilteringRatio(double preCl
         return this;
     }
 
+    public CloneAssemblerParameters setPreClusteringCountFilteringRatio(double preClusteringCountFilteringRatio) {
+        this.preClusteringCountFilteringRatio = preClusteringCountFilteringRatio;
+        return this;
+    }
+
 
     public CloneAssemblerParameters setAddReadsCountOnClustering(boolean addReadsCountOnClustering) {
         this.addReadsCountOnClustering = addReadsCountOnClustering;
@@ -289,7 +297,7 @@ public CloneAssemblerParameters clone() {
                 qualityAggregationType,
                 cloneClusteringParameters == null ? null : cloneClusteringParameters.clone(),
                 cloneFactoryParameters.clone(), separateByV, separateByJ, separateByC,
-                maximalPreClusteringRatio, preClusteringScoreFilteringRatio, addReadsCountOnClustering, badQualityThreshold, maxBadPointsPercent,
+                maximalPreClusteringRatio, preClusteringScoreFilteringRatio, preClusteringCountFilteringRatio, addReadsCountOnClustering, badQualityThreshold, maxBadPointsPercent,
                 mappingThreshold, minimalQuality);
     }
 
@@ -307,6 +315,7 @@ public boolean equals(Object o) {
         if (separateByC != that.separateByC) return false;
         if (Double.compare(that.maximalPreClusteringRatio, maximalPreClusteringRatio) != 0) return false;
         if (Double.compare(that.preClusteringScoreFilteringRatio, preClusteringScoreFilteringRatio) != 0) return false;
+        if (Double.compare(that.preClusteringCountFilteringRatio, preClusteringCountFilteringRatio) != 0) return false;
         if (addReadsCountOnClustering != that.addReadsCountOnClustering) return false;
         if (badQualityThreshold != that.badQualityThreshold) return false;
         if (Double.compare(that.maxBadPointsPercent, maxBadPointsPercent) != 0) return false;
@@ -338,6 +347,8 @@ public int hashCode() {
         result = 31 * result + (int) (temp ^ (temp >>> 32));
         temp = Double.doubleToLongBits(preClusteringScoreFilteringRatio);
         result = 31 * result + (int) (temp ^ (temp >>> 32));
+        temp = Double.doubleToLongBits(preClusteringCountFilteringRatio);
+        result = 31 * result + (int) (temp ^ (temp >>> 32));
         result = 31 * result + (addReadsCountOnClustering ? 1 : 0);
         result = 31 * result + (int) badQualityThreshold;
         temp = Double.doubleToLongBits(maxBadPointsPercent);

diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java
@@ -321,10 +321,11 @@ private void clusterizeBranches(int[] points, List<VariantBranch> branches) {
                 sumWeight += weights[j - i - 1];
             }
 
-            for (int j = i + 1; j < branches.size(); ++j) {
-                VariantBranch cluster = branches.get(j);
-                cluster.count += branch.count * weights[j - i - 1] / sumWeight;
-            }
+            if (sumWeight != 0.0)
+                for (int j = i + 1; j < branches.size(); ++j) {
+                    VariantBranch cluster = branches.get(j);
+                    cluster.count += branch.count * weights[j - i - 1] / sumWeight;
+                }
 
             if (report != null)
                 report.onVariantClustered(branch);

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java
@@ -552,6 +552,9 @@ public CaseSensitiveNucleotideSequence getIncompleteFeature(GeneFeature geneFeat
                     if (lLast.begin > rLast.end)
                         return null;
 
+                    if (lLast.germline || rLast.germline)
+                        return null;
+
 //                    assert lHit.getGene().getGeneType() == GeneType.Variable;
 //                    if (!lHit
 //                            .getPartitioningForTarget(lLast.iTarget)

diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java
@@ -165,6 +165,11 @@ public long getJChimeras() {
         return jChimeras.get();
     }
 
+    @JsonProperty("chainUsage")
+    public ChainUsageStats getChainUsage() {
+        return chainStats;
+    }
+
     @JsonProperty("realignedWithForcedNonFloatingBound")
     public long getRealignedWithForcedNonFloatingBound() {
         return realignedWithForcedNonFloatingBound.get();

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java
@@ -29,17 +29,24 @@
  */
 package com.milaboratory.mixcr.cli;
 
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import com.milaboratory.mixcr.basictypes.VDJCObject;
 import io.repseq.core.Chains;
 
+import java.io.IOException;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicLong;
 
 /**
  * Created by poslavsky on 08/11/2016.
  */
-final class ChainUsageStats implements Report {
+@JsonSerialize(using = ChainUsageStats.Serializer.class)
+public final class ChainUsageStats implements Report {
     final AtomicLong chimeras = new AtomicLong(0);
     final AtomicLong total = new AtomicLong(0);
     final ConcurrentHashMap<Chains, AtomicLong> counters = new ConcurrentHashMap<>();
@@ -80,4 +87,22 @@ public void writeReport(ReportHelper helper) {
         for (Map.Entry<Chains, AtomicLong> ch : counters.entrySet())
             helper.writePercentAndAbsoluteField(ch.getKey().toString() + " chains", ch.getValue(), total);
     }
+
+    public static final class Serializer extends JsonSerializer<ChainUsageStats> {
+        @Override
+        public void serialize(ChainUsageStats value, JsonGenerator jgen, SerializerProvider provider) throws IOException, JsonProcessingException {
+            jgen.writeStartObject();
+            jgen.writeNumberField("total", value.total.longValue());
+            jgen.writeNumberField("chimeras", value.chimeras.longValue());
+            jgen.writeObjectFieldStart("chains");
+            for (Map.Entry<Chains, AtomicLong> entry : value.counters.entrySet()) {
+                String chains = entry.getKey().toString();
+                if (chains.isEmpty())
+                    chains = "X";
+                jgen.writeNumberField(chains, entry.getValue().longValue());
+            }
+            jgen.writeEndObject();
+            jgen.writeEndObject();
+        }
+    }
 }
diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java
@@ -146,6 +146,11 @@ public long getReadsDroppedWithClones() {
         return readsDroppedWithClones.get();
     }
 
+    @JsonProperty("clonalChainUsage")
+    public ChainUsageStats getClonalChainUsage() {
+        return chainStats;
+    }
+
     @Override
     public void onNewCloneCreated(CloneAccumulator accumulator) {
         clonesCreated.incrementAndGet();

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java
@@ -117,7 +117,7 @@ protected List<String> getOutputFiles() {
     public String reportFile = null;
 
     @Option(description = CommonDescriptions.JSON_REPORT,
-            names = {"--json-report"})
+            names = {"-j", "--json-report"})
     public String jsonReport = null;
 
     @Option(description = "V/D/J/C gene library",

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java
@@ -42,6 +42,7 @@
 import picocli.CommandLine.Option;
 import picocli.CommandLine.Parameters;
 
+import java.io.File;
 import java.lang.reflect.Field;
 import java.util.*;
 import java.util.stream.Collectors;
@@ -623,6 +624,9 @@ public void validate() {
         super.validate();
         if (report == null)
             warn("NOTE: report file is not specified, using " + getReport() + " to write report.");
+        if (new File(outputNamePattern()).exists())
+            throwValidationException("Output file name prefix, matches the existing file name. Most probably you " +
+                    "specified paired-end file names but forgot to specify output file name prefix.", false);
     }
 
     @Override

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java
@@ -76,7 +76,7 @@ public void setThreads(int threads) {
     public String reportFile;
 
     @Option(description = CommonDescriptions.JSON_REPORT,
-            names = {"--json-report"})
+            names = {"-j", "--json-report"})
     public String jsonReport;
 
     @Option(description = "Show buffer statistics.",

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java
@@ -92,7 +92,7 @@ public void setThreads(int threads) {
     public String debugReportFile;
 
     @Option(description = CommonDescriptions.JSON_REPORT,
-            names = {"--json-report"})
+            names = {"-j", "--json-report"})
     public String jsonReport = null;
 
     public FullSeqAssemblerParameters getFullSeqAssemblerParameters() {

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java
@@ -60,7 +60,7 @@ public class CommandAssemblePartialAlignments extends ACommandWithSmartOverwrite
     public String reportFile;
 
     @Option(description = CommonDescriptions.JSON_REPORT,
-            names = {"--json-report"})
+            names = {"-j", "--json-report"})
     public String jsonReport = null;
 
     @Option(description = "Write only overlapped sequences (needed for testing).",

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java
@@ -71,7 +71,7 @@ public class CommandExtend extends ACommandWithSmartOverwriteWithSingleInputMiXC
     public String reportFile;
 
     @Option(description = CommonDescriptions.JSON_REPORT,
-            names = {"--json-report"})
+            names = {"-j", "--json-report"})
     public String jsonReport = null;
 
     @Option(description = "Quality score value to assign imputed sequences",

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java
@@ -37,7 +37,7 @@ private CommonDescriptions() {
             "Species (organism), as specified in library file or taxon id.%n" +
                     "Possible values: hs, HomoSapiens, musmusculus, mmu, hsa, 9606, 10090 etc.";
 
-    public static final String REPORT = "Report file (human readable version, see --json-report for machine readable report)";
+    public static final String REPORT = "Report file (human readable version, see -j / --json-report for machine readable report)";
 
     public static final String JSON_REPORT = "JSON formatted report file";
 

diff --git a/src/main/resources/parameters/assembler_parameters.json b/src/main/resources/parameters/assembler_parameters.json
@@ -9,6 +9,7 @@
         "separateByC": false,
         "maximalPreClusteringRatio": 1.0,
         "preClusteringScoreFilteringRatio": 2.0,
+        "preClusteringCountFilteringRatio": 2.0,
         "cloneClusteringParameters": {
             "searchDepth": 2,
             "allowedMutationsInNRegions": 1,

diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java
@@ -54,7 +54,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge
         CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12,
                 QualityAggregationType.Average,
                 new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)),
-                factoryParameters, true, true, false, 0.4, 2.0, true, (byte) 20, .8, "2", (byte) 15);
+                factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2", (byte) 15);
 
         String str = GlobalObjectMappers.PRETTY.writeValueAsString(params);
         //System.out.println(str);
@@ -82,7 +82,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge
         CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12,
                 QualityAggregationType.Average,
                 new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)),
-                factoryParameters, true, true, false, 0.4, 2.0, true, (byte) 20, .8, "2of6", (byte) 15);
+                factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15);
 
         String str = GlobalObjectMappers.PRETTY.writeValueAsString(params);
         //System.out.println(str);

diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java
@@ -118,7 +118,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException
                 new GeneFeature[]{GeneFeature.CDR3}, 12,
                 QualityAggregationType.Average,
                 new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)),
-                factoryParameters, true, true, false, 0.4,2.0, true, (byte) 20, .8, "2 of 6", (byte) 15);
+                factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2 of 6", (byte) 15);
 
         System.out.println(GlobalObjectMappers.toOneLine(assemblerParameters));
 
@@ -130,7 +130,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException
         CloneSet cloneSet = assemblerRunner.getCloneSet(null);
 
         ByteArrayOutputStream bos = new ByteArrayOutputStream();
-        try(ClnsWriter writer = new ClnsWriter(null, cloneSet, bos)){
+        try (ClnsWriter writer = new ClnsWriter(null, cloneSet, bos)) {
             writer.write();
         }
 

diff --git a/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java b/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java
@@ -0,0 +1,47 @@
+/*
+ * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail
+ * (here and after addressed as Inventors)
+ * All Rights Reserved
+ *
+ * Permission to use, copy, modify and distribute any part of this program for
+ * educational, research and non-profit purposes, by non-profit institutions
+ * only, without fee, and without a written agreement is hereby granted,
+ * provided that the above copyright notice, this paragraph and the following
+ * three paragraphs appear in all copies.
+ *
+ * Those desiring to incorporate this work into commercial products or use for
+ * commercial purposes should contact MiLaboratory LLC, which owns exclusive
+ * rights for distribution of this program for commercial purposes, using the
+ * following email address: licensing@milaboratory.com.
+ *
+ * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
+ * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS,
+ * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS
+ * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
+ * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO
+ * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A
+ * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY
+ * PATENT, TRADEMARK OR OTHER RIGHTS.
+ */
+package com.milaboratory.mixcr.cli;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.milaboratory.util.GlobalObjectMappers;
+import io.repseq.core.Chains;
+import org.junit.Test;
+
+public class ChainUsageStatsTest {
+    @Test
+    public void serializationTest() throws JsonProcessingException {
+        ChainUsageStats stats = new ChainUsageStats();
+        stats.total.incrementAndGet();
+        stats.total.incrementAndGet();
+        stats.chimeras.incrementAndGet();
+        stats.getCounter(Chains.TRB).incrementAndGet();
+        System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(stats));
+    }
+}
diff --git a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java b/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java
@@ -98,7 +98,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge
         CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12,
                 QualityAggregationType.Average,
                 new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)),
-                factoryParameters, true, true, false, 0.4,2.0, true, (byte) 20, .8, "2of6", (byte) 15);
+                factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15);
 
         CloneAssemblerParameters override = JsonOverrider.override(
                 params,
@@ -108,7 +108,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge
         CloneAssemblerParameters expected = new CloneAssemblerParameters(new GeneFeature[]{new GeneFeature(GeneFeature.CDR1, -5, +6), GeneFeature.CDR2}, 12,
                 QualityAggregationType.Average,
                 new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)),
-                factoryParameters, true, true, false, 0.4,2.0, true, (byte) 20, .8, "2of6", (byte) 15);
+                factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15);
 
 
         Assert.assertEquals(expected, override);
@@ -127,7 +127,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge
         CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12,
                 QualityAggregationType.Average,
                 new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)),
-                factoryParameters, true, true, false, 0.4,2.0, true, (byte) 20, .8, "2of6", (byte) 15);
+                factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15);
 
         CloneAssemblerParameters override = JsonOverrider.override(
                 params,