diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index d0ea7d416..d404cb387 100644 --- 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(); + } }