Class org.broadinstitute.hellbender.engine.ReadsPathDataSourceUnitTest

90

tests

0

failures

0

ignored

0.097s

duration

100%

successful

Tests

Test Duration Result
testCustomSamReaderFactory 0.001s passed
testDefaultSamReaderValidationStringency 0.001s passed
testHandleEmptyFileList 0s passed
testHandleNonExistentFile 0.001s passed
testHandleNullFile 0s passed
testHandleNullFileList 0s passed
testHandleUnindexedFileQuery 0.001s passed
testHandleUnindexedFileWithIntervals 0s passed
testIdentifySortOrder[0]([], unsorted) 0s passed
testIdentifySortOrder[1]([SAMFileHeader{VN=1.6, SO=unknown}], unknown) 0s passed
testIdentifySortOrder[2]([SAMFileHeader{VN=1.6, SO=coordinate}], coordinate) 0s passed
testIdentifySortOrder[3]([SAMFileHeader{VN=1.6, SO=queryname}], queryname) 0s passed
testIdentifySortOrder[4]([SAMFileHeader{VN=1.6, SO=unknown}, SAMFileHeader{VN=1.6, SO=unknown}], unknown) 0s passed
testIdentifySortOrder[5]([SAMFileHeader{VN=1.6, SO=coordinate}, SAMFileHeader{VN=1.6, SO=coordinate}], coordinate) 0s passed
testIdentifySortOrder[6]([SAMFileHeader{VN=1.6, SO=queryname}, SAMFileHeader{VN=1.6, SO=queryname}], queryname) 0s passed
testIdentifySortOrder[7]([SAMFileHeader{VN=1.6, SO=unknown}, SAMFileHeader{VN=1.6, SO=coordinate}, SAMFileHeader{VN=1.6, SO=queryname}], unsorted) 0s passed
testIdentifySortOrder[8]([SAMFileHeader{VN=1.6, SO=coordinate}, SAMFileHeader{VN=1.6, SO=coordinate}, SAMFileHeader{VN=1.6, SO=queryname}], unsorted) 0s passed
testManuallySpecifiedIndicesEmptyIndexList[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test2.bam], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test1.bam.bai, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test2.bam.bai]) 0s passed
testManuallySpecifiedIndicesNullIndexListOK[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test2.bam], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test1.bam.bai, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test2.bam.bai]) 0.001s passed
testManuallySpecifiedIndicesWithCustomReaderFactoryAndNullWrappers[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test2.bam], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test1.bam.bai, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test2.bam.bai]) 0.002s passed
testManuallySpecifiedIndicesWithCustomReaderFactory[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test2.bam], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test1.bam.bai, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test2.bam.bai]) 0.001s passed
testManuallySpecifiedIndicesWrongNumberOfIndices[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test2.bam], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test1.bam.bai, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test2.bam.bai]) 0.001s passed
testManuallySpecifiedIndices[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/reads_data_source_test2.bam], [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test1.bam.bai, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/readIndexTest/indices/reads_data_source_test2.bam.bai]) 0.004s passed
testMergedQueryWithFileSpecificContigs[0]([Lorg.broadinstitute.hellbender.utils.SimpleInterval;@12bd2630, [Ljava.lang.String;@1546a589, [I@726c1889) 0.020s passed
testMergedQueryWithFileSpecificContigs[1]([Lorg.broadinstitute.hellbender.utils.SimpleInterval;@22e3d222, [Ljava.lang.String;@241410c5, [I@46f7c5c1) 0.006s passed
testMergedQueryWithFileSpecificContigs[2]([Lorg.broadinstitute.hellbender.utils.SimpleInterval;@14cd9288, [Ljava.lang.String;@4433e4e2, [I@1bdaa13c) 0.007s passed
testMergedQueryWithFileSpecificContigs[3]([Lorg.broadinstitute.hellbender.utils.SimpleInterval;@2b360641, [Ljava.lang.String;@779d7ff4, [I@33a9f5b0) 0.006s passed
testMultipleFilesCompleteTraversal[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam], [a, b, l, c, m, n, d, e, o, f, p, g, h, q, r, s, t, i, j, u, v, k]) 0.001s passed
testMultipleFilesCompleteTraversal[1]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [l, m, n, o, p, q, r, s, w, t, x, u, v, y, z]) 0.001s passed
testMultipleFilesCompleteTraversal[2]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [a, b, c, d, e, f, g, h, w, x, i, j, y, k, z]) 0s passed
testMultipleFilesCompleteTraversal[3]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [a, b, l, c, m, n, d, e, o, f, p, g, h, q, r, s, w, t, x, i, j, u, v, y, k, z]) 0.002s passed
testMultipleFilesQueryByInterval[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], 1:285-1000, [c, m, n, d]) 0.002s passed
testMultipleFilesQueryByInterval[1]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], 3:200-300, [t, x, i]) 0.002s passed
testMultipleFilesQueryByInterval[2]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], 1:9000-11000, [o]) 0.001s passed
testMultipleFilesQueryByInterval[3]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], 3:1-16000, [w, t, x, i, j, u, v]) 0.002s passed
testMultipleFilesQueryByInterval[4]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], 2:10000-12000, []) 0.001s passed
testMultipleFilesTraversalWithIntervals[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [1:205-207, 1:400-1000, 4:500-704], [a, b, l, n, d, y, k]) 0.002s passed
testMultipleFilesTraversalWithIntervals[1]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [4:500-704, 1:400-1000, 1:205-207], [a, b, l, n, d, y, k]) 0.002s passed
testMultipleFilesTraversalWithIntervals[2]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [2:500-600, 2:2099-2200, 3:50-100, 3:300-500], [f, p, g, s, w, i, j, u]) 0.001s passed
testMultipleFilesTraversalWithIntervals[3]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [1:1-300, 1:100-500, 1:200-600], [a, b, l, c, m, n]) 0.001s passed
testMultipleFilesTraversalWithIntervals[4]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [1:11000-12000, 3:1000-2000], []) 0.002s passed
testMultipleFilesTraversalWithIntervals[5]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam], [1:1-16000, 2:1-16000, 3:1-16000, 4:1-16000], [a, b, l, c, m, n, d, e, o, f, p, g, h, q, r, s, w, t, x, i, j, u, v, y, k, z]) 0.001s passed
testQueryUnmapped[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [u1, u2, u3, u4, u5]) 0.001s passed
testQueryUnmapped[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, [g, h, h, i, i]) 0.001s passed
testSingleFileCompleteTraversal[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [a, b, c, d, e, f, g, h, i, j, k]) 0.001s passed
testSingleFileCompleteTraversal[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, [l, m, n, o, p, q, r, s, t, u, v]) 0s passed
testSingleFileCompleteTraversal[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam, [w, x, y, z]) 0.001s passed
testSingleFileQueryByIntervalSerialIteration[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 1:200-209, [a, b]) 0.001s passed
testSingleFileQueryByIntervalSerialIteration[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 1:285-1100, [c, d, e]) 0s passed
testSingleFileQueryByIntervalSerialIteration[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 2:550-649, [f, g]) 0.001s passed
testSingleFileQueryByIntervalSerialIteration[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 3:399-400, [j]) 0s passed
testSingleFileQueryByIntervalSerialIteration[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 4:100-200, []) 0s passed
testSingleFileQueryByIntervalSerialIteration[5](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 4:600-699, []) 0.001s passed
testSingleFileQueryByInterval[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 1:200-209, [a, b]) 0s passed
testSingleFileQueryByInterval[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 1:285-1100, [c, d, e]) 0s passed
testSingleFileQueryByInterval[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 2:550-649, [f, g]) 0.001s passed
testSingleFileQueryByInterval[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 3:399-400, [j]) 0s passed
testSingleFileQueryByInterval[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 4:100-200, []) 0.001s passed
testSingleFileQueryByInterval[5](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, 4:600-699, []) 0s passed
testSingleFileSerialTraversal[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [a, b, c, d, e, f, g, h, i, j, k]) 0.001s passed
testSingleFileSerialTraversal[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam, [l, m, n, o, p, q, r, s, t, u, v]) 0s passed
testSingleFileSerialTraversal[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test3.bam, [w, x, y, z]) 0.001s passed
testSingleFileTraversalWithIntervals[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [1:200-210, 2:550-700, 4:700-701], [a, b, c, f, g, h, k]) 0.001s passed
testSingleFileTraversalWithIntervals[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [1:205-209, 3:400-410], [a, b, j]) 0s passed
testSingleFileTraversalWithIntervals[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [1:999-1200, 2:530-625, 4:1000-1200], [d, e, f, g]) 0.001s passed
testSingleFileTraversalWithIntervals[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [1:900-1100, 1:1000-1200], [d, e]) 0s passed
testSingleFileTraversalWithIntervals[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [1:1000-1099], [d]) 0.001s passed
testSingleFileTraversalWithIntervals[5](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [1:2000-3000, 1:4000-5000, 2:1000-2000], []) 0s passed
testSupportsSerialIteration[0]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam], true) 0.001s passed
testSupportsSerialIteration[1]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test2.bam], true) 0.001s passed
testSupportsSerialIteration[2]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/invalid_coord_sort_order.sam], false) 0s passed
testSupportsSerialIteration[3]([/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/invalid_coord_sort_order.sam], false) 0.001s passed
testTraversalWithUnmappedReads[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [1:200-1000], false, [a, b, c, d]) 0.001s passed
testTraversalWithUnmappedReads[10](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, null, true, []) 0s passed
testTraversalWithUnmappedReads[11](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [], true, []) 0s passed
testTraversalWithUnmappedReads[12](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, false, [a, b, c, d, e, f, g, h, i, j, k, u1, u2, u3, u4, u5]) 0.001s passed
testTraversalWithUnmappedReads[13](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [], false, [a, b, c, d, e, f, g, h, i, j, k, u1, u2, u3, u4, u5]) 0s passed
testTraversalWithUnmappedReads[14](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, [20:10000011-10000013], false, [a, b, c, d, e, f, f]) 0.001s passed
testTraversalWithUnmappedReads[15](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, [20:10000011-10000013], true, [a, b, c, d, e, f, f, g, h, h, i, i]) 0.001s passed
testTraversalWithUnmappedReads[16](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, [20:10000009-10000011], false, [a, b, c, d, e]) 0s passed
testTraversalWithUnmappedReads[17](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, [20:10000009-10000011], true, [a, b, c, d, e, g, h, h, i, i]) 0s passed
testTraversalWithUnmappedReads[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [1:200-1000], true, [a, b, c, d, u1, u2, u3, u4, u5]) 0s passed
testTraversalWithUnmappedReads[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [1:200-1000, 2:500-700, 4:700-701], false, [a, b, c, d, f, g, h, k]) 0.001s passed
testTraversalWithUnmappedReads[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [1:200-1000, 2:500-700, 4:700-701], true, [a, b, c, d, f, g, h, k, u1, u2, u3, u4, u5]) 0s passed
testTraversalWithUnmappedReads[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [1:3000-4000], false, []) 0.001s passed
testTraversalWithUnmappedReads[5](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [1:3000-4000], true, [u1, u2, u3, u4, u5]) 0s passed
testTraversalWithUnmappedReads[6](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [1:3000-4000], true, []) 0.001s passed
testTraversalWithUnmappedReads[7](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, [1:200-1000], true, [a, b, c, d]) 0s passed
testTraversalWithUnmappedReads[8](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, true, [u1, u2, u3, u4, u5]) 0s passed
testTraversalWithUnmappedReads[9](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, [], true, [u1, u2, u3, u4, u5]) 0s passed

Standard error

21:17:52.808 WARN  ReadsPathDataSource - Inputs have different sort orders. Assuming unsorted sorted reads for all of them.
21:17:52.809 WARN  ReadsPathDataSource - Inputs have different sort orders. Assuming unsorted sorted reads for all of them.
21:17:52.809 WARN  ReadsPathDataSource - Inputs have different sort orders. Assuming unsorted sorted reads for all of them.