analyze params sanity check

CHANGELOG_CURRENT

@@ -1,4 +1,5 @@
 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`
+Added shortcut for `--json-report` = `-j`
+Sanity check for common mistake in `analyze` parameters

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