Class org.broadinstitute.hellbender.engine.FeatureManagerUnitTest

all > org.broadinstitute.hellbender.engine > FeatureManagerUnitTest
29

tests
0

failures
0

ignored
0.051s

duration
100%

successful

Tests

Test Duration Result
testDetectCorrectFileFormat[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf, class htsjdk.variant.vcf.VCFCodec) 0.003s passed
testDetectCorrectFileFormat[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf, class htsjdk.variant.vcf.VCF3Codec) 0.002s passed
testDetectCorrectFileFormat[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf, class htsjdk.variant.bcf2.BCF2Codec) 0.002s passed
testDetectCorrectFileFormat[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed, class htsjdk.tribble.bed.BEDCodec) 0.002s passed
testDetectCorrectFileFormat[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_table_file.table, class org.broadinstitute.hellbender.utils.codecs.table.TableCodec) 0.002s passed
testDetectFeatureTypeFromFeatureInputField[0](variantContextFeatureInput, class htsjdk.variant.variantcontext.VariantContext) 0.001s passed
testDetectFeatureTypeFromFeatureInputField[1](variantContextListFeatureInput, class htsjdk.variant.variantcontext.VariantContext) 0s passed
testDetectFeatureTypeFromFeatureInputField[2](bedFeatureInput, interface htsjdk.tribble.bed.BEDFeature) 0.001s passed
testDetectFeatureTypeFromFeatureInputField[3](bedListFeatureInput, interface htsjdk.tribble.bed.BEDFeature) 0.001s passed
testDetectParameterlessFeatureInputs[0](parameterlessFeatureInput) 0.001s passed
testDetectParameterlessFeatureInputs[1](parameterlessListFeatureInput) 0.001s passed
testDetectUnsupportedFileFormat 0.001s passed
testEmptySequenceDictionary 0.003s passed
testGetAllSequenceDictionaries 0.006s passed
testHandleRequestForNonExistentFeatureInput 0.001s passed
testHandleRequestForValidFeatureInputIterator 0.004s passed
testHandleRequestForValidFeatureInputIteratorWithoutIndex 0.002s passed
testHandleRequestForValidFeatureInputs 0.004s passed
testIsFeatureFile[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf, true) 0.001s passed
testIsFeatureFile[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf, true) 0s passed
testIsFeatureFile[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf, true) 0s passed
testIsFeatureFile[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed, true) 0.001s passed
testIsFeatureFile[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_table_file.table, true) 0.001s passed
testIsFeatureFile[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/unsupported_format_file, false) 0.001s passed
testIsFeatureFile[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, false) 0.001s passed
testIsFeatureFile[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/non_existent_file.bed, false) 0s passed
testRestrictCodecSelectionToWrongFeatureType 0.001s passed
testSequenceDictionary 0.004s passed
testTwoSequenceDictionaries 0.004s passed

Standard error

14:51:03.825 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf
14:51:03.826 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf
14:51:03.828 INFO  FeatureManager - Using codec VCF3Codec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf
14:51:03.828 INFO  FeatureManager - Using codec VCF3Codec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf
14:51:03.830 INFO  FeatureManager - Using codec BCF2Codec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf
14:51:03.831 INFO  FeatureManager - Using codec BCF2Codec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf
14:51:03.832 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed
14:51:03.833 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed
14:51:03.834 INFO  FeatureManager - Using codec TableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_table_file.table
14:51:03.835 INFO  FeatureManager - Using codec TableCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_table_file.table
14:51:03.844 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf
14:51:03.847 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf
14:51:03.849 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed
14:51:03.850 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:51:03.850 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
14:51:03.853 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf
14:51:03.855 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed
14:51:03.858 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.wo-idx.vcf
14:51:03.860 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf
14:51:03.861 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed
14:51:03.872 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
14:51:03.875 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
14:51:03.877 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf