fix for #222

public/biopet-tools/src/test/resources/VEP_oneline.vcf

 ##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="Sat Jun 14 16:58:07 CEST 2014",Epoch=1402757887567,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/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/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.snp.recal) tranches_file=/data/DIV5/KG/kg_wes_mr/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="Sat Jun 14 17:01:08 CEST 2014",Epoch=1402758068552,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/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/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.indel.recal) tranches_file=/data/DIV5/KG/kg_wes_mr/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/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Child_7006504.ready.bam, /data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Mother_7006508.ready.bam, /data/DIV5/KG/kg_wes_mr/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="Sat Jun 14 15:20:24 CEST 2014",Epoch=1402752024377,Version=3.1-1-g07a4bf8>
-##HaplotypeCallerCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Sat Jun 14 22:28:02 CEST 2014",Epoch=1402777682364,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/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/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.snp.recal) tranches_file=/data/DIV5/KG/kg_wes_mr/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="Sat Jun 14 22:31:13 CEST 2014",Epoch=1402777873043,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/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/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.indel.recal) tranches_file=/data/DIV5/KG/kg_wes_mr/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/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Child_7006504.ready.bam, /data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Mother_7006508.ready.bam, /data/DIV5/KG/kg_wes_mr/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="Sat Jun 14 15:26:18 CEST 2014",Epoch=1402752378803,Version=3.1-1-g07a4bf8>
 ##INFO=<ID=DN,Number=1,Type=Integer,Description="inDbSNP">
 ##INFO=<ID=DT,Number=0,Type=Flag,Description="in1000Genomes">
 ##INFO=<ID=DA,Number=1,Type=String,Description="allelesDBSNP">
@@ -164,5 +158,5 @@
 ##contig=<ID=chrUn_gl000248,length=39786>
 ##contig=<ID=chrUn_gl000249,length=38502>
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|AA_MAF|EA_MAF|ALLELE_NUM|DISTANCE|STRAND|CLIN_SIG|SYMBOL|SYMBOL_SOURCE|GMAF|HGVSc|HGVSp|AFR_MAF|AMR_MAF|ASN_MAF|EUR_MAF|PUBMED">
-#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	871042	rs199537431	C	CA	1541.12	PASS	FG=intron;FD=unknown;GM=NM_152486.2;GL=SAMD11;CP=0.000;CG=-1.630;CN=2294,3274,30362,112930;DSP=107;AC=2;AF=0.333;AN=6;BaseQRankSum=4.068;DB;DP=124;FS=1.322;MLEAC=2;MLEAF=0.333;MQ=60.0;MQ0=0;MQRankSum=-0.197;QD=19.03;RPA=1,2;RU=A;ReadPosRankSum=-0.424;STR;VQSLOD=0.079;culprit=FS;GATKCaller=UG,HC;CSQ=A|ENSESTG00000013623|ENSESTT00000034081|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||||A:0.0078|ENSESTT00000034081.1:c.306-110_306-109insA||||||,A|CCDS2.2|CCDS2.2|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||||A:0.0078|CCDS2.2:c.306-110_306-109insA||||||,A|ENSESTG00000013623|ENSESTT00000034116|Transcript|upstream_gene_variant||||||rs199537431|||1|3610|1||||A:0.0078|||||||,A|ENSESTG00000013623|ENSESTT00000034091|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||||A:0.0078|ENSESTT00000034091.1:c.306-110_306-109insA||||||,A|ENSESTG00000013623|ENSESTT00000034102|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||||A:0.0078|ENSESTT00000034102.1:c.29-110_29-109insA||||||,A|148398|XM_005244723.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244723.1:c.306-110_306-109insA||||||,A|148398|XM_005244724.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244724.1:c.306-110_306-109insA||||||,A|148398|XM_005244725.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244725.1:c.306-110_306-109insA||||||,A|148398|NM_152486.2|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|NM_152486.2:c.306-110_306-109insA||||||,A|148398|XM_005244727.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244727.1:c.306-110_306-109insA||||||,A|148398|XM_005244726.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244726.1:c.306-110_306-109insA||||||	GT:AD:DP:GQ:PL	0/1:24,21:45:99:838,0,889	0/1:17,19:36:99:744,0,603	0/0:42,0:43:99:0,126,1717

public/biopet-tools/src/test/resources/unvepped.vcf

 ##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

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala

@@ -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"
 
   }
 

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala

@@ -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))
   }