Warn instead of throwing when querying intervals that were not in Gen…

…omicsDBImport (#8987)

* Switch to logging a warning instead of an exception for intervals in a query that were not part of GenomicsDBImport
* upgrade GenomicsDB 1.5.3 -> 1.5.4
* fixes #8415

build.gradle

@@ -63,7 +63,7 @@ final barclayVersion = System.getProperty('barclay.version','5.0.0')
 final sparkVersion = System.getProperty('spark.version', '3.5.0')
 final hadoopVersion = System.getProperty('hadoop.version', '3.3.6')
 final disqVersion = System.getProperty('disq.version','0.3.8')
-final genomicsdbVersion = System.getProperty('genomicsdb.version','1.5.3')
+final genomicsdbVersion = System.getProperty('genomicsdb.version','1.5.4')
 final bigQueryVersion = System.getProperty('bigQuery.version', '2.35.0')
 final bigQueryStorageVersion = System.getProperty('bigQueryStorage.version', '2.47.0')
 final guavaVersion = System.getProperty('guava.version', '32.1.3-jre')

src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java

@@ -132,6 +132,11 @@ public final class GenomicsDBImportIntegrationTest extends CommandLineProgramTes
         new SimpleInterval("chr20", 17970001, 17980000),
         new SimpleInterval("chr20", 17980001, 17981445)
     ));
+    private static final ArrayList<SimpleInterval> INCLUDES_NON_IMPORTED_INTERVALS = new ArrayList<SimpleInterval>(Arrays.asList(
+        new SimpleInterval("chr2", 1, 100),
+        new SimpleInterval("chr20", 17960187, 17981445),
+        new SimpleInterval("chr22", 1, 100)
+    ));
     private static final ArrayList<SimpleInterval> MULTIPLE_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS =
         new ArrayList<SimpleInterval>(Arrays.asList(
             new SimpleInterval("chr20", 17960187, 17969999),
@@ -226,6 +231,13 @@ public void testGenomicsDBImportFileInputsWithMultipleIntervals() throws IOExcep
         testGenomicsDBImporter(LOCAL_GVCFS, MULTIPLE_INTERVALS, COMBINED_MULTI_INTERVAL, b38_reference_20_21, true, 1);
     }
 
+    @Test
+    public void testGenomicsDBImportFileInputsIncludeNonImportedIntervals() throws IOException {
+      final String workspace = createTempDir("genomicsdb-tests-").getAbsolutePath() + "/workspace";
+      writeToGenomicsDB(LOCAL_GVCFS, INTERVAL, workspace, 0, false, 0, 1, false, false, false, 0, true);
+      checkGenomicsDBAgainstExpected(workspace, INCLUDES_NON_IMPORTED_INTERVALS, COMBINED, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
+    }
+
     @Test
     public void testGenomicsDBImportFileInputsWithMultipleIntervalsNativeReader() throws IOException {
         testGenomicsDBImporter(LOCAL_GVCFS, MULTIPLE_INTERVALS, COMBINED_MULTI_INTERVAL, b38_reference_20_21, true, 1, true);