| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/spark/ |
| H A D | DataprocIntegrationTest.java | 52 final String outputPath = BucketUtils.getTempFilePath(getGCPTestStaging(), ".bam"); in printReadSparkOnDataproc()
85 final String outputPath = BucketUtils.getTempFilePath(getGCPTestStaging(), ".vcf"); in printVariantsOnDataproc()
108 final String bamOut = BucketUtils.getTempFilePath(getGCPTestStaging(), ".bam"); in markDuplicatesSparkOnDataproc()
109 final String metricsOut = BucketUtils.getTempFilePath(getGCPTestStaging(), ".metrics"); in markDuplicatesSparkOnDataproc()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/ |
| H A D | PrintVariantsSparkIntegrationTest.java | 34 final String outputPrefix = outputToGCS ? getGCPTestStaging() : "testGCSInputsAndOutputs"; in testGCSInputsAndOutputs()
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| H A D | PrintReadsSparkIntegrationTest.java | 63 final String outputPrefix = outputToGCS ? getGCPTestStaging() : "testGCSInputsAndOutputs"; in testGCSInputsAndOutputsWithSparkNio()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/nio/ |
| H A D | NioFileCopierWithProgessMeterTestUtils.java | 37 …ath = BucketUtils.getPathOnGcs(BucketUtils.getTempFilePath(BaseTest.getGCPTestStaging() + destBase… in getDestPathFromPseudoUrl()
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| H A D | GcsNioIntegrationTest.java | 51 getGCPTestStaging() +"GcsNioIntegrationTest-writePrivateFile-test", ".txt"); in writePrivateFile()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/testutils/ |
| H A D | DataprocTestUtils.java | 95 final String gcpTestStaging = BaseTest.getGCPTestStaging(); in launchGatkTool()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/metrics/ |
| H A D | MetricsUtilsTest.java | 37 {getGCPTestStaging()}, in getMetricsPaths()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ReadUtilsIntegrationTest.java | 51 …final String outputPathName = BucketUtils.getTempFilePath(getGCPTestStaging() + "samWriterTest", o… in testCreatePathSAMWriter()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/gcs/ |
| H A D | BucketUtilsUnitTest.java | 152 …final String intermediate = BucketUtils.randomRemotePath(getGCPTestStaging(), "test-copy-empty", "… in testCopyAndDeleteGCS()
211 final String gcsSubDir = BucketUtils.randomRemotePath(getGCPTestStaging(), "dir-", "/"); in testDirSizeGCS()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/tsv/ |
| H A D | SimpleCSVWriterWrapperWithHeaderUnitTest.java | 24 getGCPTestStaging() + "testWriteToBucketPathEquivalentToLocalPath", ".tsv")); in testWriteToBucketPathEquivalentToLocalPath()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ |
| H A D | ApplyBQSRIntegrationTest.java | 155 …final String outString = BucketUtils.getTempFilePath(getGCPTestStaging() + "tmp/testApplyBQSRCloud… in testApplyBQSRCloud()
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| /dports/biology/gatk/gatk-4.2.0.0/src/testUtils/java/org/broadinstitute/hellbender/testutils/ |
| H A D | BaseTest.java | 123 public static String getGCPTestStaging() { in getGCPTestStaging() method in BaseTest
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/ |
| H A D | AbstractPrintReadsIntegrationTest.java | 335 final String outputPrefix = outputToGCS ? getGCPTestStaging() : "testGCSInputsAndOutputs"; in testGCSInputsAndOutputs()
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| H A D | IndexFeatureFileIntegrationTest.java | 61 getGCPTestStaging() +"testIndexOnCloud", ".vcf"); in testVCFIndexOnCloud()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ |
| H A D | SelectVariantsIntegrationTest.java | 957 getGCPTestStaging() +"testSelectVariants_SimpleSelection", ".vcf"); in testSampleSelectionOnNio()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/ |
| H A D | GenomicsDBImportIntegrationTest.java | 1216 final String workspace = BucketUtils.randomRemotePath(getGCPTestStaging(), "", "") + "/"; in testWriteToAndQueryFromGCS()
1225 final String workspace = BucketUtils.randomRemotePath(getGCPTestStaging(), "", "") + "/"; in testWriteToExistingGCSDirectory()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/io/ |
| H A D | IOUtilsUnitTest.java | 723 final String gcsFolder = BucketUtils.randomRemotePath(getGCPTestStaging(), "test-dir", ""); in testDeleteRecursivelyGCS()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
| H A D | HaplotypeCallerIntegrationTest.java | 662 getGCPTestStaging() + "testBamoutProducesReasonablySizedOutput", ".bam")); in testBamoutOnGcs()
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