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`analyze` params sanity check

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dbolotin committed Aug 2, 2019
1 parent dcee49e commit 299285c66a44ad972a9c53b811dcd8295a785b6a
Showing with 6 additions and 1 deletion.
  1. +2 −1 CHANGELOG_CURRENT
  2. +4 −0 src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java
@@ -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
@@ -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

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