Class org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodecUnitTest

all > org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable > XsvLocatableTableCodecUnitTest
31

tests
0

failures
0

ignored
0.047s

duration
100%

successful

Tests

Test Duration Result
testBadContigColumnNames[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader_error_contig_equals_start.config, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader.tsv) 0.010s passed
testBadContigColumnNames[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader_error_contig_equals_end.config, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader.tsv) 0.002s passed
testCanDecodeFileChecks[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test2.config, true) 0s passed
testCanDecodeFileChecks[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader_multiple_columns.config, true) 0.001s passed
testCanDecodeFileChecks[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/NON_EXISTENT_FILE, false) 0s passed
testCanDecodeFileChecks[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_fails_decode_checks.config, false) 0.001s passed
testCanDecodeFileChecks[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_fails_decode_checks2.config, false) 0.001s passed
testCanDecode[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test.config, true) 0.001s passed
testCanDecode[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test2.config, true) 0.001s passed
testCanDecode[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_no_config.csv, false) 0s passed
testCanDecode[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test3.config, true) 0.001s passed
testDecodeCharsetFailure[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_mixed_encodings.config) 0.001s passed
testDecodeMultipleChoiceHeaders[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader_multiple_columns.config, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader.tsv, [SECOND_XSV_NAME_chr, SECOND_XSV_NAME_start, SECOND_XSV_NAME_end]) 0.001s passed
testDecodeMultipleChoiceHeaders[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader_multiple_columns_no_name.config, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_samfileheader.tsv, [chr, start, end]) 0.001s passed
testDecodeMultipleChoiceHeaders[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_same_startend.config, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_same_startend.csv, [XSV_LOCATABLE_TEST_NAME_chr, XSV_LOCATABLE_TEST_NAME_Position, XSV_LOCATABLE_TEST_NAME_Position]) 0.002s passed
testDecodeMultipleChoiceHeaders[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_same_startend_no_name.config, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_same_startend.csv, [chr, Position, Position]) 0s passed
testDecode[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test.config, [XsvTableFeature{contigColumn=1, startColumn=3, endColumn=4, locationColumnRemoveIndiciesInOrder=[4, 3, 1], dataSourceName='XSV_LOCATABLE_TEST_NAME', contig='chr19', start=8959519, end=9092018, columnNames=[XSV_LOCATABLE_TEST_NAME_Villain, XSV_LOCATABLE_TEST_NAME_chr, XSV_LOCATABLE_TEST_NAME_test_val, XSV_LOCATABLE_TEST_NAME_start, XSV_LOCATABLE_TEST_NAME_end, XSV_LOCATABLE_TEST_NAME_Bond], columnValues=[Blofeld, chr19, test_val_chr19, 8959519, 9092018, Connery]}, XsvTableFeature{contigColumn=1, startColumn=3, endColumn=4, locationColumnRemoveIndiciesInOrder=[4, 3, 1], dataSourceName='XSV_LOCATABLE_TEST_NAME', contig='chr3', start=178866310, end=178957882, columnNames=[XSV_LOCATABLE_TEST_NAME_Villain, XSV_LOCATABLE_TEST_NAME_chr, XSV_LOCATABLE_TEST_NAME_test_val, XSV_LOCATABLE_TEST_NAME_start, XSV_LOCATABLE_TEST_NAME_end, XSV_LOCATABLE_TEST_NAME_Bond], columnValues=[Largo, chr3, test_val_chr3, 178866310, 178957882, Dalton]}]) 0.011s passed
testDecode[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test2.config, [XsvTableFeature{contigColumn=1, startColumn=2, endColumn=4, locationColumnRemoveIndiciesInOrder=[4, 2, 1], dataSourceName='SECOND_XSV_NAME', contig='chr3', start=178866310, end=178957882, columnNames=[SECOND_XSV_NAME_Car_Maker, SECOND_XSV_NAME_chr, SECOND_XSV_NAME_start, SECOND_XSV_NAME_Tire_Maker, SECOND_XSV_NAME_end, SECOND_XSV_NAME_Parent_Company], columnValues=[Lamborghini, chr3, 178866310, Michelin, 178957882, Audi]}, XsvTableFeature{contigColumn=1, startColumn=2, endColumn=4, locationColumnRemoveIndiciesInOrder=[4, 2, 1], dataSourceName='SECOND_XSV_NAME', contig='chr19', start=8959519, end=9092018, columnNames=[SECOND_XSV_NAME_Car_Maker, SECOND_XSV_NAME_chr, SECOND_XSV_NAME_start, SECOND_XSV_NAME_Tire_Maker, SECOND_XSV_NAME_end, SECOND_XSV_NAME_Parent_Company], columnValues=[Ferrari, chr19, 8959519, Pirelli, 9092018, Fiat]}]) 0.001s passed
testDecode[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test3.config, [XsvTableFeature{contigColumn=1, startColumn=3, endColumn=4, locationColumnRemoveIndiciesInOrder=[4, 3, 1], dataSourceName='XSV_LOCATABLE_TEST_NAME', contig='chr19', start=8959519, end=9092018, columnNames=[XSV_LOCATABLE_TEST_NAME_Villain, XSV_LOCATABLE_TEST_NAME_chr, XSV_LOCATABLE_TEST_NAME_test_val, XSV_LOCATABLE_TEST_NAME_start, XSV_LOCATABLE_TEST_NAME_end, XSV_LOCATABLE_TEST_NAME_Bond], columnValues=[Blofeld, chr19, test_val_chr19, 8959519, 9092018, Connery]}, XsvTableFeature{contigColumn=1, startColumn=3, endColumn=4, locationColumnRemoveIndiciesInOrder=[4, 3, 1], dataSourceName='XSV_LOCATABLE_TEST_NAME', contig='chr3', start=178866310, end=178957882, columnNames=[XSV_LOCATABLE_TEST_NAME_Villain, XSV_LOCATABLE_TEST_NAME_chr, XSV_LOCATABLE_TEST_NAME_test_val, XSV_LOCATABLE_TEST_NAME_start, XSV_LOCATABLE_TEST_NAME_end, XSV_LOCATABLE_TEST_NAME_Bond], columnValues=[Largo, chr3, test_val_chr3, 178866310, 178957882, Dalton]}]) 0.001s passed
testDecode[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test4.config, [XsvTableFeature{contigColumn=1, startColumn=3, endColumn=4, locationColumnRemoveIndiciesInOrder=[4, 3, 1], dataSourceName='XSV_LOCATABLE_TEST_NAME', contig='chr19', start=8959519, end=9092018, columnNames=[XSV_LOCATABLE_TEST_NAME_Villain, XSV_LOCATABLE_TEST_NAME_chr, XSV_LOCATABLE_TEST_NAME_test_val, XSV_LOCATABLE_TEST_NAME_start, XSV_LOCATABLE_TEST_NAME_end, XSV_LOCATABLE_TEST_NAME_Bond], columnValues=[Blofeld, chr19, test_val_chr19, 8959519, 9092018, Connery]}, XsvTableFeature{contigColumn=1, startColumn=3, endColumn=4, locationColumnRemoveIndiciesInOrder=[4, 3, 1], dataSourceName='XSV_LOCATABLE_TEST_NAME', contig='chr3', start=178866310, end=178957882, columnNames=[XSV_LOCATABLE_TEST_NAME_Villain, XSV_LOCATABLE_TEST_NAME_chr, XSV_LOCATABLE_TEST_NAME_test_val, XSV_LOCATABLE_TEST_NAME_start, XSV_LOCATABLE_TEST_NAME_end, XSV_LOCATABLE_TEST_NAME_Bond], columnValues=[Largo, chr3, test_val_chr3, 178866310, 178957882, Dalton]}]) 0.003s passed
testFalseCanDecodeFromMixedPreambles 0s passed
testGetAndValidateConfigFileContents[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test.config, {origin_location=GATK Github Test Area, start_column=3, version=TESTING, preprocessing_script=NA, src_file=xsv_locatable_test.csv, contig_column=1, xsv_delimiter=,, name=XSV_LOCATABLE_TEST_NAME, end_column=4}) 0s passed
testGetAndValidateConfigFileContents[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test2.config, {origin_location=GATK Github Test Area, start_column=2, version=TESTING, preprocessing_script=NA, src_file=xsv_locatable_test2.tsv, contig_column=1, xsv_delimiter= , name=SECOND_XSV_NAME, end_column=4}) 0.001s passed
testGetConfigFilePath[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test.config, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test.config) 0s passed
testGetConfigFilePath[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test2.config, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test2.config) 0s passed
testNotFoundInList 0.002s passed
testReadActualHeader[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test.config, [XSV_LOCATABLE_TEST_NAME_Villain, XSV_LOCATABLE_TEST_NAME_chr, XSV_LOCATABLE_TEST_NAME_test_val, XSV_LOCATABLE_TEST_NAME_start, XSV_LOCATABLE_TEST_NAME_end, XSV_LOCATABLE_TEST_NAME_Bond]) 0s passed
testReadActualHeader[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test2.config, [SECOND_XSV_NAME_Car_Maker, SECOND_XSV_NAME_chr, SECOND_XSV_NAME_start, SECOND_XSV_NAME_Tire_Maker, SECOND_XSV_NAME_end, SECOND_XSV_NAME_Parent_Company]) 0s passed
testRenderSamFileHeaderFromNoPreamble 0.001s passed
testRenderSamFileHeaderFromSamFileHeaderPreamble 0.003s passed
testTrueCanDecodeFromMissingColumn 0.001s passed

Standard error

WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
20:34:39.205 ERROR XsvLocatableTableCodec - Config file for datasource (file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/utils/codecs/xsvLocatableTable/xsv_locatable_test_fails_decode_checks2.config) does not contain required key: origin_location
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING	2025-02-10 20:34:39	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream