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Display warning when using large interval lists with GenomicsDBImport. #5102

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Aug 14, 2018
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Display warning when using large interval lists with GenomicsDBImport. #5102

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9 changes: 9 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -146,6 +146,7 @@ public final class GenomicsDBImport extends GATKTool {
public static final String VALIDATE_SAMPLE_MAP_LONG_NAME = "validate-sample-name-map";
public static final String VCF_INITIALIZER_THREADS_LONG_NAME = "reader-threads";
public static final String MAX_NUM_INTERVALS_TO_IMPORT_IN_PARALLEL = "max-num-intervals-to-import-in-parallel";
public static final int INTERVAL_LIST_SIZE_WARNING_THRESHOLD = 100;

@Argument(fullName = WORKSPACE_ARG_LONG_NAME,
doc = "Workspace for GenomicsDB. Must be a POSIX file system path, but can be a relative path." +
Expand Down Expand Up @@ -703,6 +704,14 @@ private void initializeIntervals() {

intervals = new ArrayList<>();
final List<SimpleInterval> simpleIntervalList = intervalArgumentCollection.getIntervals(intervalDictionary);
if (simpleIntervalList.size() > INTERVAL_LIST_SIZE_WARNING_THRESHOLD) {
logger.warn(String.format(
"A large number of intervals were specified. " +
"Using more than %d intervals in a single import is not recommended and can cause performance to suffer. " +
"It is recommended that intervals be aggregated together.",
INTERVAL_LIST_SIZE_WARNING_THRESHOLD)
);
}
simpleIntervalList.forEach(interval -> intervals.add(new ChromosomeInterval(interval.getContig(),
interval.getStart(), interval.getEnd())));
} else {
Expand Down