| Test |
Duration |
Result |
| testCopyConstructor[0](someFile.bam, null, null, null, null) |
0s |
passed |
| testCopyConstructor[1](someFile.bam, sometag, null, sometag, null) |
0s |
passed |
| testCopyConstructor[2](someFile.bam, null, {tag1=value1}, null, {tag1=value1}) |
0.001s |
passed |
| testCopyConstructor[3](someFile.bam, sometag, {tag1=value1}, sometag, {tag1=value1}) |
0s |
passed |
| testCopyConstructor[4](someFile.bam, null, {tag1=value1, tag2=value2}, null, {tag1=value1, tag2=value2}) |
0s |
passed |
| testCopyConstructor[5](someFile.bam, sometag, {tag1=value1, tag2=value2}, sometag, {tag1=value1, tag2=value2}) |
0s |
passed |
| testEquals[0](someFile.bam, null, null, null, null) |
0s |
passed |
| testEquals[1](someFile.bam, sometag, null, sometag, null) |
0s |
passed |
| testEquals[2](someFile.bam, null, {tag1=value1}, null, {tag1=value1}) |
0s |
passed |
| testEquals[3](someFile.bam, sometag, {tag1=value1}, sometag, {tag1=value1}) |
0s |
passed |
| testEquals[4](someFile.bam, null, {tag1=value1, tag2=value2}, null, {tag1=value1, tag2=value2}) |
0s |
passed |
| testEquals[5](someFile.bam, sometag, {tag1=value1, tag2=value2}, sometag, {tag1=value1, tag2=value2}) |
0s |
passed |
| testGetBaseName[0](localFile, localFile) |
0s |
passed |
| testGetBaseName[10](aFile.fasta.gz, aFile.fasta) |
0s |
passed |
| testGetBaseName[11](.fasta.gz, .fasta) |
0s |
passed |
| testGetBaseName[12](gs://hellbender/test/somefile, somefile) |
0s |
passed |
| testGetBaseName[13](gs://hellbender/test/somefile?query=param, somefile) |
0.001s |
passed |
| testGetBaseName[14](aFile.fasta.gz, aFile.fasta) |
0s |
passed |
| testGetBaseName[15](.fasta.gz, .fasta) |
0s |
passed |
| testGetBaseName[1](localFile.bam, localFile) |
0s |
passed |
| testGetBaseName[2](localFile.BAM, localFile) |
0s |
passed |
| testGetBaseName[3](localFile., localFile) |
0s |
passed |
| testGetBaseName[4](/localFile.bam, localFile) |
0s |
passed |
| testGetBaseName[5](/localFile., localFile) |
0s |
passed |
| testGetBaseName[6](gs://bucket/aFile.bam, aFile) |
0s |
passed |
| testGetBaseName[7](gs://hellbender/test/resources/aFile.adam, aFile) |
0s |
passed |
| testGetBaseName[8](gs://hellbender/test/resources/aFile.fasta, aFile) |
0s |
passed |
| testGetBaseName[9](http://bucket/aFile.bam?query=param, aFile) |
0s |
passed |
| testGetExtension[0](localFile.bam, .bam) |
0.001s |
passed |
| testGetExtension[1](localFile.BAM, .BAM) |
0s |
passed |
| testGetExtension[2](/localFile.bam, .bam) |
0s |
passed |
| testGetExtension[3](gs://bucket/aFile.bam, .bam) |
0s |
passed |
| testGetExtension[4](gs://hellbender/test/resources/aFile.adam, .adam) |
0s |
passed |
| testGetExtension[5](gs://hellbender/test/resources/aFile.fasta, .fasta) |
0s |
passed |
| testGetExtension[6](http://bucket/aFile.bam?query=param, .bam) |
0.001s |
passed |
| testGetExtension[7](aFile.fasta.gz, .gz) |
0s |
passed |
| testGetExtension[8](.fasta.gz, .gz) |
0s |
passed |
| testGetExtension[9](/.fasta, .fasta) |
0s |
passed |
| testGetInputStream[0](src/test/resources/org/broadinstitute/hellbender/tools/testTextFile.txt, Test file.) |
0.001s |
passed |
| testGetInputStream[1](/gatkCloneMountPoint/./src/test/resources/org/broadinstitute/hellbender/tools/testTextFile.txt, Test file.) |
0s |
passed |
| testGetInputStream[2](file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/testTextFile.txt, Test file.) |
0s |
passed |
| testGetInputStream[3](src/test/resources/org/broadinstitute/hellbender/tools/testDirWith#InName/testTextFile.txt, Test file.) |
0s |
passed |
| testGetInputStream[4](file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/testDirWith%23InName/testTextFile.txt, Test file.) |
0s |
passed |
| testGetOutputStream[0](/tmp/testOutputStream16966528342156911160.txt) |
0.001s |
passed |
| testGetOutputStream[1](file:///tmp/testOutputStream8083003538647038576.txt) |
0s |
passed |
| testHasExtension[0](localFile.bam, .bam) |
0s |
passed |
| testHasExtension[10](aFile.fasta.gz, .fasta.gz) |
0s |
passed |
| testHasExtension[11](.fasta.gz, .gz) |
0s |
passed |
| testHasExtension[12](.fasta.gz, .fasta.gz) |
0s |
passed |
| testHasExtension[1](localFile.BAM, .BAM) |
0s |
passed |
| testHasExtension[2](localFile.BAM, .bam) |
0s |
passed |
| testHasExtension[3](localFile.bam, .BAM) |
0s |
passed |
| testHasExtension[4](/localFile.bam, .bam) |
0s |
passed |
| testHasExtension[5](gs://bucket/aFile.bam, .bam) |
0s |
passed |
| testHasExtension[6](gs://hellbender/test/resources/aFile.adam, .adam) |
0s |
passed |
| testHasExtension[7](gs://hellbender/test/resources/aFile.fasta, .fasta) |
0.001s |
passed |
| testHasExtension[8](http://bucket/aFile.bam?query=param, .bam) |
0s |
passed |
| testHasExtension[9](aFile.fasta.gz, .gz) |
0s |
passed |
| testIllegalHasExtension[0](localFile, .) |
0s |
passed |
| testIllegalHasExtension[1](localFile., .) |
0s |
passed |
| testIllegalHasExtension[2](localFile.ext, .) |
0s |
passed |
| testIllegalHasExtension[3](localFile.ext, a) |
0s |
passed |
| testInstalledNonDefaultFileSystem |
0.008s |
passed |
| testIsBam[0](my.bam, true) |
0s |
passed |
| testIsBam[1](my.Bam, true) |
0s |
passed |
| testIsBam[2](my.BAM, true) |
0s |
passed |
| testIsBam[3](http://bucket/aFile.bam?query=param, true) |
0s |
passed |
| testIsBam[4](my.sam, false) |
0s |
passed |
| testIsBam[5](my.cram, false) |
0s |
passed |
| testIsCram[0](my.cram, true) |
0s |
passed |
| testIsCram[1](my.Cram, true) |
0s |
passed |
| testIsCram[2](my.CRAM, true) |
0s |
passed |
| testIsCram[3](http://bucket/aFile.cram?query=param, true) |
0s |
passed |
| testIsCram[4](my.sam, false) |
0s |
passed |
| testIsCram[5](my.bam, false) |
0s |
passed |
| testIsFasta[0](/gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.2bit, false) |
0s |
passed |
| testIsFasta[1](file:///gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.2bit, false) |
0s |
passed |
| testIsFasta[2](/gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz, true) |
0s |
passed |
| testIsFasta[3](file:///gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz, true) |
0s |
passed |
| testIsFasta[4](gs://hellbender/test/resources/large/human_g1k_v37.20.21.2bit, false) |
0s |
passed |
| testIsFasta[5](gs://hellbender/test/resources/large/human_g1k_v37.20.21.fasta, true) |
0s |
passed |
| testIsFasta[6](gs://hellbender/test/resources/large/human_g1k_v37.20.21.fasta?query=param, true) |
0s |
passed |
| testIsHadoopURL[0](hdfs://someFile, true) |
0s |
passed |
| testIsHadoopURL[1](file://someFile.bam, false) |
0s |
passed |
| testIsHadoopURL[2](someFile.bam, false) |
0s |
passed |
| testIsNIO[0](localFile.bam, file:///gatkCloneMountPoint/localFile.bam, true, true) |
0s |
passed |
| testIsNIO[10](file:localFile.bam, file:localFile.bam, true, false) |
0s |
passed |
| testIsNIO[11](file:/localFile.bam, file:/localFile.bam, true, true) |
0s |
passed |
| testIsNIO[12](file://localFile.bam, file://localFile.bam, true, false) |
0s |
passed |
| testIsNIO[13](file:///localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testIsNIO[14](file:path/to/localFile.bam, file:path/to/localFile.bam, true, false) |
0s |
passed |
| testIsNIO[15](file:/path/to/localFile.bam, file:/path/to/localFile.bam, true, true) |
0s |
passed |
| testIsNIO[16](file://path/to/localFile.bam, file://path/to/localFile.bam, true, false) |
0s |
passed |
| testIsNIO[17](file://localhost/to/localFile.bam, file://localhost/to/localFile.bam, true, false) |
0s |
passed |
| testIsNIO[18](file:///path/to/localFile.bam, file:///path/to/localFile.bam, true, true) |
0s |
passed |
| testIsNIO[19](gs://file.bam, gs://file.bam, true, true) |
0.001s |
passed |
| testIsNIO[1](/localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testIsNIO[20](gs://bucket/file.bam, gs://bucket/file.bam, true, true) |
0s |
passed |
| testIsNIO[21](gs:///bucket/file.bam, gs:///bucket/file.bam, true, false) |
0s |
passed |
| testIsNIO[22](gs://auth/bucket/file.bam, gs://auth/bucket/file.bam, true, true) |
0s |
passed |
| testIsNIO[23](gs://hellbender/test/resources/, gs://hellbender/test/resources/, true, true) |
0s |
passed |
| testIsNIO[24](gcs://abucket/bucket, gcs://abucket/bucket, false, false) |
0s |
passed |
| testIsNIO[25](gendb://somegdb, gendb://somegdb, false, false) |
0s |
passed |
| testIsNIO[26](chr1:1-100, chr1:1-100, false, false) |
0.001s |
passed |
| testIsNIO[27](jimfs:file.bam, jimfs:file.bam, true, false) |
0s |
passed |
| testIsNIO[28](jimfs:/file.bam, jimfs:/file.bam, true, false) |
0s |
passed |
| testIsNIO[29](jimfs://file.bam, jimfs://file.bam, true, false) |
0s |
passed |
| testIsNIO[2](/localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testIsNIO[30](jimfs:///file.bam, jimfs:///file.bam, true, false) |
0s |
passed |
| testIsNIO[31](jimfs://root/file.bam, jimfs://root/file.bam, true, false) |
0s |
passed |
| testIsNIO[32](project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:///gatkCloneMountPoint/project/gvcf-pcr/23232_1%231/1.g.vcf.gz, true, true) |
0s |
passed |
| testIsNIO[33](file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz, true, false) |
0s |
passed |
| testIsNIO[34](file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, true, false) |
0s |
passed |
| testIsNIO[35](file:///project/gvcf-pcr/23232_1%231/1.g.vcf.g, file:///project/gvcf-pcr/23232_1%231/1.g.vcf.g, true, true) |
0s |
passed |
| testIsNIO[3](/path/to/localFile.bam, file:///path/to/localFile.bam, true, true) |
0s |
passed |
| testIsNIO[4](/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:///project/gvcf-pcr/23232_1%231/1.g.vcf.gz, true, true) |
0s |
passed |
| testIsNIO[5](path/to/localFile.bam, file:///gatkCloneMountPoint/path/to/localFile.bam, true, true) |
0s |
passed |
| testIsNIO[6](/, file:///, true, true) |
0s |
passed |
| testIsNIO[7](., file:///gatkCloneMountPoint/./, true, true) |
0.001s |
passed |
| testIsNIO[8](../., file:///gatkCloneMountPoint/.././, true, true) |
0s |
passed |
| testIsNIO[9](, file:///gatkCloneMountPoint/, true, true) |
0s |
passed |
| testIsPathInvalid[0](file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz) |
0s |
passed |
| testIsPathInvalid[1](file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz) |
0s |
passed |
| testIsPathInvalid[2](hdfs://userinfo@host:80/path/to/file.bam) |
0.047s |
passed |
| testIsPathInvalid[3](unknownscheme://foobar) |
0.002s |
passed |
| testIsPathInvalid[4](gendb://adb) |
0.001s |
passed |
| testIsPathInvalid[5](gcs://abucket/bucket) |
0.002s |
passed |
| testIsPathInvalid[6](file://nonexistent_authority/path/to/file.bam) |
0s |
passed |
| testIsPath[0](localFile.bam, file:///gatkCloneMountPoint/localFile.bam, true, true) |
0s |
passed |
| testIsPath[10](file:localFile.bam, file:localFile.bam, true, false) |
0s |
passed |
| testIsPath[11](file:/localFile.bam, file:/localFile.bam, true, true) |
0s |
passed |
| testIsPath[12](file://localFile.bam, file://localFile.bam, true, false) |
0s |
passed |
| testIsPath[13](file:///localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testIsPath[14](file:path/to/localFile.bam, file:path/to/localFile.bam, true, false) |
0s |
passed |
| testIsPath[15](file:/path/to/localFile.bam, file:/path/to/localFile.bam, true, true) |
0s |
passed |
| testIsPath[16](file://path/to/localFile.bam, file://path/to/localFile.bam, true, false) |
0s |
passed |
| testIsPath[17](file://localhost/to/localFile.bam, file://localhost/to/localFile.bam, true, false) |
0s |
passed |
| testIsPath[18](file:///path/to/localFile.bam, file:///path/to/localFile.bam, true, true) |
0s |
passed |
| testIsPath[19](gs://file.bam, gs://file.bam, true, true) |
0.004s |
passed |
| testIsPath[1](/localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testIsPath[20](gs://bucket/file.bam, gs://bucket/file.bam, true, true) |
0s |
passed |
| testIsPath[21](gs:///bucket/file.bam, gs:///bucket/file.bam, true, false) |
0s |
passed |
| testIsPath[22](gs://auth/bucket/file.bam, gs://auth/bucket/file.bam, true, true) |
0s |
passed |
| testIsPath[23](gs://hellbender/test/resources/, gs://hellbender/test/resources/, true, true) |
0s |
passed |
| testIsPath[24](gcs://abucket/bucket, gcs://abucket/bucket, false, false) |
0.006s |
passed |
| testIsPath[25](gendb://somegdb, gendb://somegdb, false, false) |
0.004s |
passed |
| testIsPath[26](chr1:1-100, chr1:1-100, false, false) |
0.002s |
passed |
| testIsPath[27](jimfs:file.bam, jimfs:file.bam, true, false) |
0s |
passed |
| testIsPath[28](jimfs:/file.bam, jimfs:/file.bam, true, false) |
0.001s |
passed |
| testIsPath[29](jimfs://file.bam, jimfs://file.bam, true, false) |
0s |
passed |
| testIsPath[2](/localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testIsPath[30](jimfs:///file.bam, jimfs:///file.bam, true, false) |
0s |
passed |
| testIsPath[31](jimfs://root/file.bam, jimfs://root/file.bam, true, false) |
0s |
passed |
| testIsPath[32](project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:///gatkCloneMountPoint/project/gvcf-pcr/23232_1%231/1.g.vcf.gz, true, true) |
0s |
passed |
| testIsPath[33](file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz, true, false) |
0s |
passed |
| testIsPath[34](file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, true, false) |
0s |
passed |
| testIsPath[35](file:///project/gvcf-pcr/23232_1%231/1.g.vcf.g, file:///project/gvcf-pcr/23232_1%231/1.g.vcf.g, true, true) |
0s |
passed |
| testIsPath[3](/path/to/localFile.bam, file:///path/to/localFile.bam, true, true) |
0s |
passed |
| testIsPath[4](/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:///project/gvcf-pcr/23232_1%231/1.g.vcf.gz, true, true) |
0s |
passed |
| testIsPath[5](path/to/localFile.bam, file:///gatkCloneMountPoint/path/to/localFile.bam, true, true) |
0s |
passed |
| testIsPath[6](/, file:///, true, true) |
0s |
passed |
| testIsPath[7](., file:///gatkCloneMountPoint/./, true, true) |
0s |
passed |
| testIsPath[8](../., file:///gatkCloneMountPoint/.././, true, true) |
0s |
passed |
| testIsPath[9](, file:///gatkCloneMountPoint/, true, true) |
0s |
passed |
| testIsSam[0](my.sam, true) |
0s |
passed |
| testIsSam[1](my.Sam, true) |
0s |
passed |
| testIsSam[2](my.SAM, true) |
0s |
passed |
| testIsSam[3](http://bucket/aFile.sam?query=param, true) |
0s |
passed |
| testIsSam[4](my.bam, false) |
0s |
passed |
| testIsSam[5](my.cram, false) |
0s |
passed |
| testNegativeGetBaseName[0]() |
0s |
passed |
| testNegativeGetBaseName[1](/) |
0s |
passed |
| testNegativeGetBaseName[2](.) |
0s |
passed |
| testNegativeGetBaseName[3](gs://hellbender/test/resources/) |
0s |
passed |
| testNegativeGetBaseName[4](gs://hellbender/test/resources/?query=param) |
0s |
passed |
| testNegativeGetBaseName[5](/.fasta) |
0s |
passed |
| testNegativeGetBaseName[6](/name/.fasta) |
0.001s |
passed |
| testNegativeGetBaseName[7](gs://hellbender/test/resources/.fasta) |
0s |
passed |
| testNegativeGetBaseName[8](gs://hellbender/test/resources/.fasta?query=param) |
0s |
passed |
| testNegativeGetExtension[0]() |
0s |
passed |
| testNegativeGetExtension[1](/) |
0s |
passed |
| testNegativeGetExtension[2](.) |
0s |
passed |
| testNegativeGetExtension[3](gs://hellbender/test/resources/) |
0s |
passed |
| testNegativeGetExtension[4](gs://hellbender/test/resources/?query=param) |
0s |
passed |
| testNegativeGetExtension[5](localFile) |
0s |
passed |
| testNegativeGetExtension[6](localFile.) |
0s |
passed |
| testNegativeGetExtension[7](/localFile.) |
0s |
passed |
| testNegativeGetExtension[8](gs://hellbender/test/resources/localFile) |
0s |
passed |
| testNegativeGetExtension[9](gs://hellbender/test/resources/localFile?query=param) |
0s |
passed |
| testNegativeHasExtension[0](/, .ext) |
0s |
passed |
| testNegativeHasExtension[10](gs://hellbender/test/resources/?query=param, .fasta) |
0.001s |
passed |
| testNegativeHasExtension[1](., .ext) |
0s |
passed |
| testNegativeHasExtension[2](localFile, .ext) |
0s |
passed |
| testNegativeHasExtension[3](localFile., .ext) |
0s |
passed |
| testNegativeHasExtension[4](localFile., .a) |
0s |
passed |
| testNegativeHasExtension[5](localFile, .a) |
0s |
passed |
| testNegativeHasExtension[6](localFile., .a) |
0s |
passed |
| testNegativeHasExtension[7](gs://hellbender/test/resources, .fasta) |
0s |
passed |
| testNegativeHasExtension[8](gs://hellbender/test/resources?query=param, .fasta) |
0s |
passed |
| testNegativeHasExtension[9](gs://hellbender/test/resources/, .fasta) |
0s |
passed |
| testPathSpecifierInvalid[0](?) |
0.001s |
passed |
| testPathSpecifier[0](localFile.bam, file:///gatkCloneMountPoint/localFile.bam, true, true) |
0s |
passed |
| testPathSpecifier[10](file:localFile.bam, file:localFile.bam, true, false) |
0s |
passed |
| testPathSpecifier[11](file:/localFile.bam, file:/localFile.bam, true, true) |
0s |
passed |
| testPathSpecifier[12](file://localFile.bam, file://localFile.bam, true, false) |
0s |
passed |
| testPathSpecifier[13](file:///localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testPathSpecifier[14](file:path/to/localFile.bam, file:path/to/localFile.bam, true, false) |
0s |
passed |
| testPathSpecifier[15](file:/path/to/localFile.bam, file:/path/to/localFile.bam, true, true) |
0.001s |
passed |
| testPathSpecifier[16](file://path/to/localFile.bam, file://path/to/localFile.bam, true, false) |
0s |
passed |
| testPathSpecifier[17](file://localhost/to/localFile.bam, file://localhost/to/localFile.bam, true, false) |
0s |
passed |
| testPathSpecifier[18](file:///path/to/localFile.bam, file:///path/to/localFile.bam, true, true) |
0s |
passed |
| testPathSpecifier[19](gs://file.bam, gs://file.bam, true, true) |
0s |
passed |
| testPathSpecifier[1](/localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testPathSpecifier[20](gs://bucket/file.bam, gs://bucket/file.bam, true, true) |
0.001s |
passed |
| testPathSpecifier[21](gs:///bucket/file.bam, gs:///bucket/file.bam, true, false) |
0s |
passed |
| testPathSpecifier[22](gs://auth/bucket/file.bam, gs://auth/bucket/file.bam, true, true) |
0s |
passed |
| testPathSpecifier[23](gs://hellbender/test/resources/, gs://hellbender/test/resources/, true, true) |
0s |
passed |
| testPathSpecifier[24](gcs://abucket/bucket, gcs://abucket/bucket, false, false) |
0s |
passed |
| testPathSpecifier[25](gendb://somegdb, gendb://somegdb, false, false) |
0s |
passed |
| testPathSpecifier[26](chr1:1-100, chr1:1-100, false, false) |
0s |
passed |
| testPathSpecifier[27](jimfs:file.bam, jimfs:file.bam, true, false) |
0s |
passed |
| testPathSpecifier[28](jimfs:/file.bam, jimfs:/file.bam, true, false) |
0s |
passed |
| testPathSpecifier[29](jimfs://file.bam, jimfs://file.bam, true, false) |
0s |
passed |
| testPathSpecifier[2](/localFile.bam, file:///localFile.bam, true, true) |
0.001s |
passed |
| testPathSpecifier[30](jimfs:///file.bam, jimfs:///file.bam, true, false) |
0s |
passed |
| testPathSpecifier[31](jimfs://root/file.bam, jimfs://root/file.bam, true, false) |
0s |
passed |
| testPathSpecifier[32](project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:///gatkCloneMountPoint/project/gvcf-pcr/23232_1%231/1.g.vcf.gz, true, true) |
0s |
passed |
| testPathSpecifier[33](file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz, true, false) |
0s |
passed |
| testPathSpecifier[34](file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, true, false) |
0s |
passed |
| testPathSpecifier[35](file:///project/gvcf-pcr/23232_1%231/1.g.vcf.g, file:///project/gvcf-pcr/23232_1%231/1.g.vcf.g, true, true) |
0s |
passed |
| testPathSpecifier[3](/path/to/localFile.bam, file:///path/to/localFile.bam, true, true) |
0s |
passed |
| testPathSpecifier[4](/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:///project/gvcf-pcr/23232_1%231/1.g.vcf.gz, true, true) |
0s |
passed |
| testPathSpecifier[5](path/to/localFile.bam, file:///gatkCloneMountPoint/path/to/localFile.bam, true, true) |
0s |
passed |
| testPathSpecifier[6](/, file:///, true, true) |
0s |
passed |
| testPathSpecifier[7](., file:///gatkCloneMountPoint/./, true, true) |
0s |
passed |
| testPathSpecifier[8](../., file:///gatkCloneMountPoint/.././, true, true) |
0s |
passed |
| testPathSpecifier[9](, file:///gatkCloneMountPoint/, true, true) |
0s |
passed |
| testStdIn |
0s |
passed |
| testStdOut |
0.001s |
passed |
| testTagsAndAttributes[0](someFile.bam, null, null, null, null) |
0s |
passed |
| testTagsAndAttributes[1](someFile.bam, sometag, null, sometag, null) |
0s |
passed |
| testTagsAndAttributes[2](someFile.bam, null, {tag1=value1}, null, {tag1=value1}) |
0s |
passed |
| testTagsAndAttributes[3](someFile.bam, sometag, {tag1=value1}, sometag, {tag1=value1}) |
0s |
passed |
| testTagsAndAttributes[4](someFile.bam, null, {tag1=value1, tag2=value2}, null, {tag1=value1, tag2=value2}) |
0s |
passed |
| testTagsAndAttributes[5](someFile.bam, sometag, {tag1=value1, tag2=value2}, sometag, {tag1=value1, tag2=value2}) |
0s |
passed |
| testToPathInvalid[0](file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz) |
0s |
passed |
| testToPathInvalid[1](file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz) |
0.001s |
passed |
| testToPathInvalid[2](hdfs://userinfo@host:80/path/to/file.bam) |
0.013s |
passed |
| testToPathInvalid[3](unknownscheme://foobar) |
0.003s |
passed |
| testToPathInvalid[4](gendb://adb) |
0.002s |
passed |
| testToPathInvalid[5](gcs://abucket/bucket) |
0.002s |
passed |
| testToPathInvalid[6](file://nonexistent_authority/path/to/file.bam) |
0s |
passed |
| testToPath[0](localFile.bam, file:///gatkCloneMountPoint/localFile.bam, true, true) |
0.001s |
passed |
| testToPath[10](file:localFile.bam, file:localFile.bam, true, false) |
0s |
passed |
| testToPath[11](file:/localFile.bam, file:/localFile.bam, true, true) |
0s |
passed |
| testToPath[12](file://localFile.bam, file://localFile.bam, true, false) |
0s |
passed |
| testToPath[13](file:///localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testToPath[14](file:path/to/localFile.bam, file:path/to/localFile.bam, true, false) |
0s |
passed |
| testToPath[15](file:/path/to/localFile.bam, file:/path/to/localFile.bam, true, true) |
0.001s |
passed |
| testToPath[16](file://path/to/localFile.bam, file://path/to/localFile.bam, true, false) |
0s |
passed |
| testToPath[17](file://localhost/to/localFile.bam, file://localhost/to/localFile.bam, true, false) |
0s |
passed |
| testToPath[18](file:///path/to/localFile.bam, file:///path/to/localFile.bam, true, true) |
0s |
passed |
| testToPath[19](gs://file.bam, gs://file.bam, true, true) |
0s |
passed |
| testToPath[1](/localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testToPath[20](gs://bucket/file.bam, gs://bucket/file.bam, true, true) |
0s |
passed |
| testToPath[21](gs:///bucket/file.bam, gs:///bucket/file.bam, true, false) |
0s |
passed |
| testToPath[22](gs://auth/bucket/file.bam, gs://auth/bucket/file.bam, true, true) |
0s |
passed |
| testToPath[23](gs://hellbender/test/resources/, gs://hellbender/test/resources/, true, true) |
0s |
passed |
| testToPath[24](gcs://abucket/bucket, gcs://abucket/bucket, false, false) |
0.002s |
passed |
| testToPath[25](gendb://somegdb, gendb://somegdb, false, false) |
0.001s |
passed |
| testToPath[26](chr1:1-100, chr1:1-100, false, false) |
0.002s |
passed |
| testToPath[27](jimfs:file.bam, jimfs:file.bam, true, false) |
0s |
passed |
| testToPath[28](jimfs:/file.bam, jimfs:/file.bam, true, false) |
0s |
passed |
| testToPath[29](jimfs://file.bam, jimfs://file.bam, true, false) |
0s |
passed |
| testToPath[2](/localFile.bam, file:///localFile.bam, true, true) |
0s |
passed |
| testToPath[30](jimfs:///file.bam, jimfs:///file.bam, true, false) |
0s |
passed |
| testToPath[31](jimfs://root/file.bam, jimfs://root/file.bam, true, false) |
0s |
passed |
| testToPath[32](project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:///gatkCloneMountPoint/project/gvcf-pcr/23232_1%231/1.g.vcf.gz, true, true) |
0s |
passed |
| testToPath[33](file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:project/gvcf-pcr/23232_1#1/1.g.vcf.gz, true, false) |
0.001s |
passed |
| testToPath[34](file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, true, false) |
0s |
passed |
| testToPath[35](file:///project/gvcf-pcr/23232_1%231/1.g.vcf.g, file:///project/gvcf-pcr/23232_1%231/1.g.vcf.g, true, true) |
0s |
passed |
| testToPath[3](/path/to/localFile.bam, file:///path/to/localFile.bam, true, true) |
0s |
passed |
| testToPath[4](/project/gvcf-pcr/23232_1#1/1.g.vcf.gz, file:///project/gvcf-pcr/23232_1%231/1.g.vcf.gz, true, true) |
0s |
passed |
| testToPath[5](path/to/localFile.bam, file:///gatkCloneMountPoint/path/to/localFile.bam, true, true) |
0s |
passed |
| testToPath[6](/, file:///, true, true) |
0s |
passed |
| testToPath[7](., file:///gatkCloneMountPoint/./, true, true) |
0s |
passed |
| testToPath[8](../., file:///gatkCloneMountPoint/.././, true, true) |
0s |
passed |
| testToPath[9](, file:///gatkCloneMountPoint/, true, true) |
0s |
passed |