def tests(self): return [ TTestCase( name="basic", input={ "positions": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.sorted.uncompressed.stdout", ), "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "bam": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.bam", ), "countOrphans": True, "noBAQ": True, "maxDepth": 10000, "minBQ": 0, }, output=TextFile.basic_test( "out", 19900, "chr17\t43044391\tG\t19\tA,A,,A.a,,A,,A..,,a\tDJCJ:FHDDBJBBJJIDDB", 187, "53c3e03c20730ff45411087444379b1b", ), ) ]
def tests(self): return [ TTestCase( name="basic", input={ "bams": [ os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.sorted.bam", ) ], "maxRecordsInRam": 5000000, "createIndex": True, "mergeSamFiles_useThreading": True, "mergeSamFiles_validationStringency": "SILENT", }, output=BamBai.basic_test( "out", 2829000, 3780, os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.bam.flagstat", ), ), ), TTestCase( name="minimal", input={ "bams": [ os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.sorted.bam", ) ], "maxRecordsInRam": 5000000, "createIndex": True, "mergeSamFiles_useThreading": True, "mergeSamFiles_validationStringency": "SILENT", }, output=self.minimal_test(), ), ]
def tests(self): return [ TTestCase( name="basic", input={ "sam": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.bwamem.stdout", ), "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "threads": 16, }, output=Bam.basic_test( "out", 2740774, os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.bam.flagstat", ), "9a6af420f287df52a122ac723f41b535", ), ), TTestCase( name="minimal", input={ "sam": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.bwamem.stdout", ), "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "threads": 16, }, output=self.minimal_test(), ), ]
def tests(self): return [ TTestCase( name="basic", input={ "bam": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.bam", ), "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "vcf": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.sorted.uncompressed.stdout", ), "samtoolsmpileup_countOrphans": True, "samtoolsmpileup_noBAQ": True, "samtoolsmpileup_maxDepth": 10000, "samtoolsmpileup_minBQ": 0, "addbamstats_type": "germline", }, output=Vcf.basic_test( "out", 69225, 230, ["GATKCommandLine"], "db09c6c37c52771bd058e32d5c6b94c1", ), ) ]
def tests(self): return [ TTestCase( name="basic", input={ "bam": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.bam", ), "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "snps_dbsnp": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.dbsnp138.BRCA1.vcf.gz", ), "snps_1000gp": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "1000G_phase1.snps.high_confidence.hg38.BRCA1.vcf.gz", ), "known_indels": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.known_indels.BRCA1.vcf.gz", ), "mills_indels": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Mills_and_1000G_gold_standard.indels.hg38.BRCA1.vcf.gz", ), "intervals": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "BRCA1.hg38.bed", ), }, output=BamBai.basic_test( "out", 2600000, 21000, os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.recalibrated.flagstat", ), ), ) ]
def tests(self): return [ TTestCase( name="basic", input={ "bam": os.path.join(BioinformaticsTool.test_data_path(), "small.bam"), }, output=[ TTestExpectedOutput( tag="out", preprocessor=TTestPreprocessor.FileMd5, operator=operator.eq, expected_value="c9c318de134643665ff1fed6cfaec49c", ), ], ) ]
def tests(self): return [ TTestCase( name="basic", input={ "reference": os.path.join( BioinformaticsTool.test_data_path(), "hg38-brca1.fasta" ), }, output=[ TTestExpectedOutput( tag="out", preprocessor=TTestPreprocessor.FileMd5, operator=operator.eq, expected_value="768915f0ceff3bae0bac0ace5f7ccad0", ), ], ) ]
def tests(self): return [ TTestCase( name="basic", input={ "bam": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.bam", ), }, output=TextFile.basic_test( "out", 410, "19486 + 0 in total (QC-passed reads + QC-failed reads)", 13, "ddbcfe52e60b925d222fb8bc1517a7a0", ), ) ]
def tests(self): return [ TTestCase( name="basic", input={ "bam": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.bam", ), "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "recalFile": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.table", ), "intervals": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "BRCA1.hg38.bed", ), }, output=BamBai.basic_test( "out", 2600000, 21000, os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.recalibrated.flagstat", ), ), ), TTestCase( name="minimal", input={ "bam": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.bam", ), "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "recalFile": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.markduped.table", ), "intervals": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "BRCA1.hg38.bed", ), }, output=self.minimal_test(), ), ]
def tests(self): return [ TTestCase( name="basic", input={ "reads": [ os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1_R1.fastq.gz", ), os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1_R2.fastq.gz", ), ], "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "markShorterSplits": True, "readGroupHeaderLine": "@RG\tID:NA12878-BRCA1\tSM:NA12878-BRCA1\tLB:NA12878-BRCA1\tPL:ILLUMINA", "threads": 16, }, output=Bam.basic_test( "out", 8628527, os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1.bwamem.flagstat", ), ), ), TTestCase( name="minimal", input={ "reads": [ os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1_R1.fastq.gz", ), os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "NA12878-BRCA1_R2.fastq.gz", ), ], "reference": os.path.join( BioinformaticsTool.test_data_path(), "wgsgermline_data", "Homo_sapiens_assembly38.chr17.fasta", ), "markShorterSplits": True, "readGroupHeaderLine": "@RG\tID:NA12878-BRCA1\tSM:NA12878-BRCA1\tLB:NA12878-BRCA1\tPL:ILLUMINA", "threads": 16, }, output=self.minimal_test(), ), ]