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fix command filterAlignments

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PoslavskySV committed Jun 19, 2019
1 parent 3ee1955 commit be747119c3bd24e865d10d61389345c60812ee3b
Showing with 3 additions and 3 deletions.
  1. +1 −1 pom.xml
  2. +2 −2 src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java
@@ -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>
@@ -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();

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