Package org.broadinstitute.hellbender.engine.spark.datasources

Failed tests

• ReadsSparkSinkUnitTest. setupMiniCluster
• ReadsSparkSourceUnitTest. testCRAMReferenceFromHDFS
• ReadsSparkSourceUnitTest. testReadFromFileAndHDFS
• VariantsSparkSinkUnitTest. setupMiniCluster

Ignored tests

• ReadsSparkSinkUnitTest. readsSinkHDFSTest[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkHDFSTest[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 1)
• ReadsSparkSinkUnitTest. readsSinkHDFSTest[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, false, 100)
• ReadsSparkSinkUnitTest. readsSinkHDFSTest[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, true, 100)
• ReadsSparkSinkUnitTest. readsSinkHDFSTest[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, false, 100)
• ReadsSparkSinkUnitTest. readsSinkHDFSTest[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, ReadsSparkSinkUnitTest2, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkHDFSTest[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, ReadsSparkSinkUnitTest3, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkHDFSTest[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram, ReadsSparkSinkUnitTest5, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, .cram, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkHDFSTest[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest6, null, .sam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 1)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, false, 100)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, true, 100)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, false, 100)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, ReadsSparkSinkUnitTest2, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, ReadsSparkSinkUnitTest3, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram, ReadsSparkSinkUnitTest5, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, .cram, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkShardedTest[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest6, null, .sam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkTest[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkTest[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 1)
• ReadsSparkSinkUnitTest. readsSinkTest[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, false, 100)
• ReadsSparkSinkUnitTest. readsSinkTest[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, true, 100)
• ReadsSparkSinkUnitTest. readsSinkTest[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, false, 100)
• ReadsSparkSinkUnitTest. readsSinkTest[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, ReadsSparkSinkUnitTest2, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkTest[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, ReadsSparkSinkUnitTest3, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkTest[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram, ReadsSparkSinkUnitTest5, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, .cram, true, true, 100)
• ReadsSparkSinkUnitTest. readsSinkTest[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest6, null, .sam, true, true, 100)
• ReadsSparkSinkUnitTest. testReadsSparkSinkNotSortingReadsToHeader
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 1)
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, false, 100)
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, true, 100)
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, false, 100)
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, ReadsSparkSinkUnitTest2, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, ReadsSparkSinkUnitTest3, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram, ReadsSparkSinkUnitTest5, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, .cram, true, true, 100)
• ReadsSparkSinkUnitTest. testSpecifyPartsDir[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest6, null, .sam, true, true, 100)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, true, 1)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, true, false, 100)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, true, 100)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest1, null, .bam, false, false, 100)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.bam, ReadsSparkSinkUnitTest2, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, ReadsSparkSinkUnitTest3, null, .bam, true, true, 100)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram, ReadsSparkSinkUnitTest5, /home/runner/work/gatk/gatk/src/test/resources/human_g1k_v37.chr17_1Mb.fasta, .cram, true, true, 100)
• ReadsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.bam, ReadsSparkSinkUnitTest6, null, .sam, true, true, 100)
• ReadsSparkSinkUnitTest. testWritingToFileURL
• VariantsSparkSinkUnitTest. testBrokenGVCFCasesAreDisallowed[0](false, .bcf)
• VariantsSparkSinkUnitTest. testBrokenGVCFCasesAreDisallowed[1](false, .bcf.gz)
• VariantsSparkSinkUnitTest. testBrokenGVCFCasesAreDisallowed[2](true, .g.bcf)
• VariantsSparkSinkUnitTest. testBrokenGVCFCasesAreDisallowed[3](true, .g.bcf.gz)
• VariantsSparkSinkUnitTest. testEnableDisableGVCFWriting[0](false, .vcf)
• VariantsSparkSinkUnitTest. testEnableDisableGVCFWriting[1](false, .vcf.gz)
• VariantsSparkSinkUnitTest. testEnableDisableGVCFWriting[2](true, .g.vcf)
• VariantsSparkSinkUnitTest. testEnableDisableGVCFWriting[3](true, .g.vcf.gz)
• VariantsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true)
• VariantsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true)
• VariantsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false)
• VariantsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true)
• VariantsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false)
• VariantsSparkSinkUnitTest. testWritingToAnExistingFileHDFS[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true)
• VariantsSparkSinkUnitTest. testWritingToFileURL[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true)
• VariantsSparkSinkUnitTest. testWritingToFileURL[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true)
• VariantsSparkSinkUnitTest. testWritingToFileURL[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false)
• VariantsSparkSinkUnitTest. testWritingToFileURL[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true)
• VariantsSparkSinkUnitTest. testWritingToFileURL[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false)
• VariantsSparkSinkUnitTest. testWritingToFileURL[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true)
• VariantsSparkSinkUnitTest. variantsSinkHDFSTest[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true)
• VariantsSparkSinkUnitTest. variantsSinkHDFSTest[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true)
• VariantsSparkSinkUnitTest. variantsSinkHDFSTest[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false)
• VariantsSparkSinkUnitTest. variantsSinkHDFSTest[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true)
• VariantsSparkSinkUnitTest. variantsSinkHDFSTest[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false)
• VariantsSparkSinkUnitTest. variantsSinkHDFSTest[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true)
• VariantsSparkSinkUnitTest. variantsSinkTest[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true)
• VariantsSparkSinkUnitTest. variantsSinkTest[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true)
• VariantsSparkSinkUnitTest. variantsSinkTest[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false)
• VariantsSparkSinkUnitTest. variantsSinkTest[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true)
• VariantsSparkSinkUnitTest. variantsSinkTest[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false)
• VariantsSparkSinkUnitTest. variantsSinkTest[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true)

Classes