fix command filterAlignments

milaboratory · Jun 19, 2019 · be74711 · be74711
1 parent 3ee1955
commit be74711
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/pom.xml b/pom.xml
@@ -46,7 +46,7 @@
         <dependency>
             <groupId>io.repseq</groupId>
             <artifactId>repseqio</artifactId>
-            <version>1.3.1</version>
+            <version>1.3.2-SNAPSHOT</version>
             <exclusions>
                 <exclusion>
                     <groupId>com.milaboratory</groupId>

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java
@@ -132,7 +132,7 @@ public AlignmentsFilter getFilter() {
     public ActionConfiguration getConfiguration() {
         return new FilterConfiguration(getChains(),
                 chimerasOnly,
-                limit, getReadIds().toArray(), getContainFeature(), getCdr3Equals());
+                limit, getReadIds() == null ? null : getReadIds().toArray(), getContainFeature(), getCdr3Equals());
     }
 
     @Override
@@ -145,7 +145,7 @@ public void run1() throws Exception {
                 sReads = new CountLimitingOutputPort<>(sReads, limit);
                 progress = SmartProgressReporter.extractProgress((CountLimitingOutputPort<?>) sReads);
             }
-            writer.header(reader.getParameters(), reader.getUsedGenes(), null);
+            writer.header(reader.getParameters(), reader.getUsedGenes(), getFullPipelineConfiguration());
             SmartProgressReporter.startProgressReport("Filtering", progress);
             int total = 0, passed = 0;
             final AlignmentsFilter filter = getFilter();