Package org.broadinstitute.hellbender.tools.spark.pipelines

Failed tests

• PrintReadsSparkIntegrationTest. doFileToFileUsingReferenceBundle

Ignored tests

• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileUsingReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[0](print_reads.sam, .sam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[10](print_reads.sorted.sam, .bam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[12](print_reads.sorted.bam, .sam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[13](print_reads.sorted.bam, .bam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[18](print_reads.sorted.queryname.sam, .sam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[19](print_reads.sorted.queryname.sam, .bam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[1](print_reads.sam, .bam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[3](print_reads.bam, .sam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[4](print_reads.bam, .bam, null)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta)
• PrintReadsSparkIntegrationTest. testFileToFileWithReferenceBundle[9](print_reads.sorted.sam, .sam, null)
• PrintReadsSparkIntegrationTest. testReadAndWriteCRAMAndReferenceOnHDFS

Classes