This fixes 454

milaboratory · Nov 16, 2018 · 29bd9ea · 29bd9ea
1 parent e7c8615
commit 29bd9ea
Showing 1 changed file with 14 additions and 7 deletions.
diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java
@@ -241,6 +241,9 @@ public void setChains(String chains) {
  "%nNOTE: this will substantially increase analysis time.")
  public boolean contigAssembly = false;
 
+ @Option(names = {"--no-export"}, description = "Do not export clonotypes to tab-delimited file.")
+ public boolean noExport = false;
+
  @Option(names = {"-r", "--report"}, description = "Report file path")
  public String report = null;
 
@@ -592,13 +595,17 @@ public void run0() throws Exception {
  fileWithClones = fileWithContigs;
  }
 
- // --- Running export
- if (!chains.equals(Chains.ALL))
- for (String chain : chains)
- mkExport(fileWithClones, fNameForExportClones(chain)).run();
- else
- for (String chain : new String[]{"ALL", "TRA", "TRB", "TRG", "TRD", "IGH", "IGK", "IGL"})
- mkExport(fileWithClones, fNameForExportClones(chain)).run();
+ if (!noExport)
+ // --- Running export
+ if (!chains.equals(Chains.ALL))
+ for (String chain : chains)
+ mkExport(fileWithClones, fNameForExportClones(chain)).run();
+ else
+ for (String chain : new String[]{"ALL", "TRA", "TRB", "TRG", "TRD", "IGH", "IGK", "IGL"}) {
+ CommandExport.CommandExportClones export = mkExport(fileWithClones, fNameForExportClones(chain));
+ export.chains = chain;
+ export.run();
+ }
  }