Class org.broadinstitute.hellbender.engine.FeatureManagerUnitTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testDetectCorrectFileFormat[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf, class htsjdk.variant.vcf.VCFCodec) | 0.002s | passed |
| testDetectCorrectFileFormat[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf, class htsjdk.variant.vcf.VCF3Codec) | 0.002s | passed |
| testDetectCorrectFileFormat[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf, class htsjdk.variant.bcf2.BCF2Codec) | 0.002s | passed |
| testDetectCorrectFileFormat[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed, class htsjdk.tribble.bed.BEDCodec) | 0.002s | passed |
| testDetectCorrectFileFormat[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_table_file.table, class org.broadinstitute.hellbender.utils.codecs.table.TableCodec) | 0.003s | passed |
| testDetectFeatureTypeFromFeatureInputField[0](variantContextFeatureInput, class htsjdk.variant.variantcontext.VariantContext) | 0.002s | 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) | 0s | passed |
| testDetectUnsupportedFileFormat | 0.001s | passed |
| testEmptySequenceDictionary | 0.003s | passed |
| testGetAllSequenceDictionaries | 0.005s | passed |
| testHandleRequestForNonExistentFeatureInput | 0.001s | passed |
| testHandleRequestForValidFeatureInputIterator | 0.005s | passed |
| testHandleRequestForValidFeatureInputIteratorWithoutIndex | 0.003s | passed |
| testHandleRequestForValidFeatureInputs | 0.004s | passed |
| testIsFeatureFile[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf, true) | 0.001s | passed |
| testIsFeatureFile[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf, true) | 0.001s | passed |
| testIsFeatureFile[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf, true) | 0.001s | passed |
| testIsFeatureFile[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed, true) | 0.001s | passed |
| testIsFeatureFile[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_table_file.table, true) | 0.001s | passed |
| testIsFeatureFile[5](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/unsupported_format_file, false) | 0.001s | passed |
| testIsFeatureFile[6](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1.bam, false) | 0.001s | passed |
| testIsFeatureFile[7](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/non_existent_file.bed, false) | 0.001s | passed |
| testRestrictCodecSelectionToWrongFeatureType | 0.001s | passed |
| testSequenceDictionary | 0.004s | passed |
| testTwoSequenceDictionaries | 0.005s | passed |
Standard error
20:25:19.855 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf 20:25:19.856 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf4_file.vcf 20:25:19.858 INFO FeatureManager - Using codec VCF3Codec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf 20:25:19.859 INFO FeatureManager - Using codec VCF3Codec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_vcf3_file.vcf 20:25:19.860 INFO FeatureManager - Using codec BCF2Codec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf 20:25:19.861 INFO FeatureManager - Using codec BCF2Codec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bcf_file.bcf 20:25:19.862 INFO FeatureManager - Using codec BEDCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed 20:25:19.863 INFO FeatureManager - Using codec BEDCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed 20:25:19.865 INFO FeatureManager - Using codec TableCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_table_file.table 20:25:19.866 INFO FeatureManager - Using codec TableCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_table_file.table 20:25:19.875 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf 20:25:19.879 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf 20:25:19.880 INFO FeatureManager - Using codec BEDCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed 20:25:19.881 WARN IndexUtils - Feature file "file:///gatkCloneMountPoint/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 20:25:19.882 WARN IndexUtils - Feature file "file:///gatkCloneMountPoint/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 20:25:19.885 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf 20:25:19.886 INFO FeatureManager - Using codec BEDCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed 20:25:19.890 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.wo-idx.vcf 20:25:19.892 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test.vcf 20:25:19.894 INFO FeatureManager - Using codec BEDCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/minimal_bed_file.bed 20:25:19.906 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf 20:25:19.910 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf 20:25:19.912 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf