Commit b4bb3fd3 authored by Sander Bollen's avatar Sander Bollen
Browse files

fix for #222

parent 911948ed
##fileformat=VCFv4.1
##reference=file:///data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta
##UnifiedGenotyperCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Wed Jul 09 06:04:23 CEST 2014",Epoch=1404878663625,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/Child_7006504.ug.chrom_merged.vcf)] recal_file=(RodBinding name=recal_file source=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.snp.recal) tranches_file=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.snp.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##UnifiedGenotyperCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Wed Jul 09 06:07:15 CEST 2014",Epoch=1404878835287,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.snp.recalibrated.vcf)] recal_file=(RodBinding name=recal_file source=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.indel.recal) tranches_file=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.indel.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##UnifiedGenotyperCommandLine=<ID=UnifiedGenotyper,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Child_7006504.ready.bam, /data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Mother_7006508.ready.bam, /data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Father_7006506.ready.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[chrM] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=20.0 standard_min_confidence_threshold_for_emitting=20.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name=dbsnp source=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/dbsnp_137.hg19_nohap.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jul 09 04:32:56 CEST 2014",Epoch=1404873176100,Version=3.1-1-g07a4bf8>
##HaplotypeCallerCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Wed Jul 09 10:12:42 CEST 2014",Epoch=1404893562589,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/Child_7006504.hc.chrom_merged.vcf)] recal_file=(RodBinding name=recal_file source=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.snp.recal) tranches_file=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.snp.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##HaplotypeCallerCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Wed Jul 09 10:15:50 CEST 2014",Epoch=1404893750488,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.snp.recalibrated.vcf)] recal_file=(RodBinding name=recal_file source=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.indel.recal) tranches_file=/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.indel.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##HaplotypeCallerCommandLine=<ID=HaplotypeCaller,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Child_7006504.ready.bam, /data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Mother_7006508.ready.bam, /data/DIV5/KG/kg_wes_mr_devel/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Father_7006506.ready.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[chrM] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bam_compression=null disable_bam_indexing=null generate_md5=null simplifyBAM=null bamWriterType=CALLED_HAPLOTYPES dbsnp=(RodBinding name=dbsnp source=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/dbsnp_137.hg19_nohap.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator] heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=20.0 standard_min_confidence_threshold_for_emitting=20.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false numPruningSamples=1 recoverDanglingHeads=false dontRecoverDanglingTails=false consensus=false emitRefConfidence=NONE GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false useFilteredReadsForAnnotations=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false pair_hmm_implementation=LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debug=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jul 09 04:32:56 CEST 2014",Epoch=1404873176271,Version=3.1-1-g07a4bf8>
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
......@@ -130,5 +124,5 @@
##contig=<ID=chrUn_gl000247,length=36422>
##contig=<ID=chrUn_gl000248,length=39786>
##contig=<ID=chrUn_gl000249,length=38502>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Child_7006504 Father_7006506 Mother_7006508
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_101 Sample_102 Sample_103
chr1 14599 . T A 35.13 VQSRTrancheSNP99.00to99.90 AC=4;AF=1.0;AN=4;BaseQRankSum=-0.736;DP=3;Dels=0.0;FS=0.0;HaplotypeScore=0.4161;MLEAC=4;MLEAF=1.0;MQ=20.77;MQ0=0;MQRankSum=0.736;QD=11.71;ReadPosRankSum=-0.736;VQSLOD=0.076;culprit=FS;GATKCaller=UG GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:0,1:1:3:32,3,0 1/1:1,1:2:3:27,3,0
......@@ -35,7 +35,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--sampleName", "Sample_101", "--reference", chrQRef_path, "--outputName", "test")
main(arguments)
}
......@@ -45,7 +45,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Sample_101", "--reference", chrQRef_path, "--outputName", "test")
main(arguments)
}
......@@ -55,7 +55,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
val arguments = Array("-V", chrQ_path, "--outputConsensus", tmppath, "--outputConsensusVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
val arguments = Array("-V", chrQ_path, "--outputConsensus", tmppath, "--outputConsensusVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Sample_101", "--reference", chrQRef_path, "--outputName", "test")
main(arguments)
}
......@@ -63,13 +63,13 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
val child = mock[Args]
when(child.sampleName) thenReturn "Child_7006504"
val father = mock[Args]
when(father.sampleName) thenReturn "Father_7006506"
val one = mock[Args]
when(one.sampleName) thenReturn "Sample_101"
val two = mock[Args]
when(two.sampleName) thenReturn "Sample_102"
getMaxAllele(record)(child) shouldBe "C-"
getMaxAllele(record)(father) shouldBe "CA"
getMaxAllele(record)(one) shouldBe "C-"
getMaxAllele(record)(two) shouldBe "CA"
}
......
......@@ -65,20 +65,20 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
hasGenotype(record, List(("Child_7006504", GenotypeType.HET))) shouldBe true
hasGenotype(record, List(("Child_7006504", GenotypeType.HOM_VAR))) shouldBe false
hasGenotype(record, List(("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
hasGenotype(record, List(("Child_7006504", GenotypeType.NO_CALL))) shouldBe false
hasGenotype(record, List(("Child_7006504", GenotypeType.MIXED))) shouldBe false
hasGenotype(record, List(("Sample_101", GenotypeType.HET))) shouldBe true
hasGenotype(record, List(("Sample_101", GenotypeType.HOM_VAR))) shouldBe false
hasGenotype(record, List(("Sample_101", GenotypeType.HOM_REF))) shouldBe false
hasGenotype(record, List(("Sample_101", GenotypeType.NO_CALL))) shouldBe false
hasGenotype(record, List(("Sample_101", GenotypeType.MIXED))) shouldBe false
hasGenotype(record, List(("Mother_7006508", GenotypeType.HET))) shouldBe false
hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_VAR))) shouldBe false
hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_REF))) shouldBe true
hasGenotype(record, List(("Mother_7006508", GenotypeType.NO_CALL))) shouldBe false
hasGenotype(record, List(("Mother_7006508", GenotypeType.MIXED))) shouldBe false
hasGenotype(record, List(("Sample_103", GenotypeType.HET))) shouldBe false
hasGenotype(record, List(("Sample_103", GenotypeType.HOM_VAR))) shouldBe false
hasGenotype(record, List(("Sample_103", GenotypeType.HOM_REF))) shouldBe true
hasGenotype(record, List(("Sample_103", GenotypeType.NO_CALL))) shouldBe false
hasGenotype(record, List(("Sample_103", GenotypeType.MIXED))) shouldBe false
hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_REF), ("Child_7006504", GenotypeType.HET))) shouldBe true
hasGenotype(record, List(("Mother_7006508", GenotypeType.HET), ("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
hasGenotype(record, List(("Sample_103", GenotypeType.HOM_REF), ("Sample_101", GenotypeType.HET))) shouldBe true
hasGenotype(record, List(("Sample_103", GenotypeType.HET), ("Sample_101", GenotypeType.HOM_REF))) shouldBe false
}
@Test def testMinQualScore() = {
......@@ -142,42 +142,42 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
mustHaveVariant(record, List("Child_7006504")) shouldBe true
mustHaveVariant(record, List("Child_7006504", "Father_7006506")) shouldBe true
mustHaveVariant(record, List("Child_7006504", "Father_7006506", "Mother_7006508")) shouldBe false
mustHaveVariant(record, List("Sample_101")) shouldBe true
mustHaveVariant(record, List("Sample_101", "Sample_102")) shouldBe true
mustHaveVariant(record, List("Sample_101", "Sample_102", "Sample_103")) shouldBe false
}
@Test def testSameGenotype() = {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
notSameGenotype(record, "Child_7006504", "Father_7006506") shouldBe false
notSameGenotype(record, "Child_7006504", "Mother_7006508") shouldBe true
notSameGenotype(record, "Father_7006506", "Mother_7006508") shouldBe true
notSameGenotype(record, "Sample_101", "Sample_102") shouldBe false
notSameGenotype(record, "Sample_101", "Sample_103") shouldBe true
notSameGenotype(record, "Sample_102", "Sample_103") shouldBe true
}
@Test def testfilterHetVarToHomVar() = {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
filterHetVarToHomVar(record, "Child_7006504", "Father_7006506") shouldBe true
filterHetVarToHomVar(record, "Child_7006504", "Mother_7006508") shouldBe true
filterHetVarToHomVar(record, "Father_7006506", "Mother_7006508") shouldBe true
filterHetVarToHomVar(record, "Sample_101", "Sample_102") shouldBe true
filterHetVarToHomVar(record, "Sample_101", "Sample_103") shouldBe true
filterHetVarToHomVar(record, "Sample_102", "Sample_103") shouldBe true
}
@Test def testDeNovo() = {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
denovoInSample(record, "Child_7006504") shouldBe false
denovoInSample(record, "Father_7006506") shouldBe false
denovoInSample(record, "Mother_7006508") shouldBe false
denovoInSample(record, "Sample_101") shouldBe false
denovoInSample(record, "Sample_102") shouldBe false
denovoInSample(record, "Sample_103") shouldBe false
}
@Test def testResToDom() = {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
val trio = new Trio("Sample_101", "Sample_102", "Sample_103")
resToDom(record, List(trio)) shouldBe false
}
......@@ -185,7 +185,7 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testTrioCompound = {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
val trio = new Trio("Sample_101", "Sample_102", "Sample_103")
trioCompound(record, List(trio))
}
......@@ -193,7 +193,7 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testDeNovoTrio = {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
val trio = new Trio("Sample_101", "Sample_102", "Sample_103")
denovoTrio(record, List(trio))
}
......
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