hotfix-4.5.x: minor bug fixed at VariantAnnotationCommandExecutor. completeInputPopulation variable is only checked if external pop freqs files are provided
@@ -287,7 +287,8 @@ public class VariantAnnotationCommandExecutor extends CommandExecutor {
private void writeRemainingPopFrequencies() throws IOException {
// For internal use only - will only be run when -Dpopulation-frequencies is activated
- if (populationFrequenciesFile != null && completeInputPopulation) {
+ if (populationFrequenciesFile != null) {
+ if (completeInputPopulation) {
DataWriter dataWriter = new JsonAnnotationWriter(output.toString(), APPEND);
dataWriter.open();
dataWriter.pre();
@@ -316,11 +317,12 @@ public class VariantAnnotationCommandExecutor extends CommandExecutor {
dataWriter.post();
dataWriter.close();
logger.info("Done.");
- } else if (!completeInputPopulation) {
+ } else {
logger.warn("complete-input-population set to false, variants in population frequencies file {} not in "
+ "input file {} will not be appended to output file.", populationFrequenciesFile, input);
}
}
+ }
private void setChromosomeList() {
