├── .gitignore ├── .gitmodules ├── .java-version ├── .travis.yml ├── LICENSE ├── Readme.md ├── changelog.txt ├── dist ├── VarDict-1.2.2.zip ├── VarDict-1.2.4.zip ├── VarDict-1.3.zip ├── VarDict-1.4.1.zip ├── VarDict-1.4.2.zip ├── VarDict-1.4.3.zip ├── VarDict-1.4.4.zip ├── VarDict-1.4.5.zip ├── VarDict-1.4.6.zip ├── VarDict-1.4.7.zip ├── VarDict-1.4.8.zip ├── VarDict-1.4.zip ├── VarDict-1.5.5.tar ├── VarDict-1.5.5.zip ├── VarDict-1.6.0.tar ├── VarDict-1.6.0.zip ├── VarDict-1.7.0.tar ├── VarDict-1.7.0.zip ├── VarDict-1.8.0.tar └── VarDict-1.8.0.zip ├── git ├── commit ├── release ├── update └── update_force ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── settings.gradle ├── src ├── main │ └── java │ │ └── com │ │ └── astrazeneca │ │ └── vardict │ │ ├── CmdParser.java │ │ ├── Configuration.java │ │ ├── Main.java │ │ ├── RegionBuilder.java │ │ ├── Utils.java │ │ ├── VarDictLauncher.java │ │ ├── collection │ │ ├── ConcurrentHashSet.java │ │ ├── DirectThreadExecutor.java │ │ ├── Tuple.java │ │ └── VariationMap.java │ │ ├── data │ │ ├── BaseInsertion.java │ │ ├── CurrentSegment.java │ │ ├── Match.java │ │ ├── Match35.java │ │ ├── ModifiedCigar.java │ │ ├── Patterns.java │ │ ├── Reference.java │ │ ├── ReferenceResource.java │ │ ├── Region.java │ │ ├── SVStructures.java │ │ ├── SamView.java │ │ ├── Side.java │ │ ├── SortPositionSclip.java │ │ ├── fishertest │ │ │ ├── FisherExact.java │ │ │ └── UnirootZeroIn.java │ │ └── scopedata │ │ │ ├── AlignedVarsData.java │ │ │ ├── CombineAnalysisData.java │ │ │ ├── GlobalReadOnlyScope.java │ │ │ ├── InitialData.java │ │ │ ├── RealignedVariationData.java │ │ │ ├── Scope.java │ │ │ └── VariationData.java │ │ ├── exception │ │ ├── RegionBoundariesException.java │ │ ├── RegionMissedSourceException.java │ │ └── WrongFastaOrBamException.java │ │ ├── modes │ │ ├── AbstractMode.java │ │ ├── AmpliconMode.java │ │ ├── SimpleMode.java │ │ ├── SomaticMode.java │ │ └── SplicingMode.java │ │ ├── modules │ │ ├── CigarModifier.java │ │ ├── CigarParser.java │ │ ├── Module.java │ │ ├── RecordPreprocessor.java │ │ ├── SAMFileParser.java │ │ ├── StructuralVariantsProcessor.java │ │ ├── ToVarsBuilder.java │ │ └── VariationRealigner.java │ │ ├── postprocessmodules │ │ ├── AmpliconPostProcessModule.java │ │ ├── SimplePostProcessModule.java │ │ └── SomaticPostProcessModule.java │ │ ├── printers │ │ ├── AmpliconOutputVariant.java │ │ ├── OutputVariant.java │ │ ├── PrinterType.java │ │ ├── SimpleOutputVariant.java │ │ ├── SomaticOutputVariant.java │ │ ├── SystemErrVariantPrinter.java │ │ ├── SystemOutVariantPrinter.java │ │ └── VariantPrinter.java │ │ └── variations │ │ ├── Cluster.java │ │ ├── Mate.java │ │ ├── Sclip.java │ │ ├── Variant.java │ │ ├── Variation.java │ │ ├── VariationUtils.java │ │ └── Vars.java └── test │ ├── java │ └── com │ │ └── astrazeneca │ │ └── vardict │ │ ├── ExceptionCounterTest.java │ │ ├── RegionBuilderTest.java │ │ ├── data │ │ └── fishertest │ │ │ └── FisherExact_Test.java │ │ ├── integrationtests │ │ ├── IntegrationTest.java │ │ └── utils │ │ │ ├── CSVReferenceManager.java │ │ │ ├── OutputFileCreator.java │ │ │ └── VarDictInput.java │ │ ├── modes │ │ └── PipelineModesTest.java │ │ ├── modules │ │ ├── AdaptorTest.java │ │ ├── CigarModifierTest.java │ │ ├── ToVarsBuilderTest.java │ │ └── VariationRealignerTest.java │ │ ├── postprocessmodules │ │ ├── AmpliconPostProcessModuleTest.java │ │ ├── SimplePostProcessModuleTest.java │ │ └── SomaticPostProcessModuleTest.java │ │ └── printers │ │ └── OutputVariantTest.java │ └── resources │ └── com │ └── astrazeneca │ └── vardict │ └── integrationtests │ ├── 172N_S7.final.chr1_sliced_SOOBE.bam │ ├── 172N_S7.final.chr1_sliced_SOOBE.bam.bai │ ├── 172T_S8.final.chr1_sliced_SOOBE.bam │ ├── 172T_S8.final.chr1_sliced_SOOBE.bam.bai │ ├── 2-364738.chr21.Negative.bam │ ├── 2-364738.chr21.Negative.bam.bai │ ├── 2-420233.chr7.Negative.bam │ ├── 2-420233.chr7.Negative.bam.bai │ ├── AMP_allele.bam │ ├── AMP_allele.bam.bai │ ├── ArgumentNA_Normal.bam │ ├── ArgumentNA_Normal.bam.bai │ ├── ArgumentNA_Tumor.bam │ ├── ArgumentNA_Tumor.bam.bai │ ├── CIGAR_Three_Indels_DLEN.bam │ ├── CIGAR_Three_Indels_DLEN.bam.bai │ ├── Colo829-18_S3-sort.bam │ ├── Colo829-18_S3-sort.bam.bai │ ├── Colo829-18_S3-sort_chrY.bam │ ├── Colo829-18_S3-sort_chrY.bam.bai │ ├── Colo829-19_S4-sort.bam │ ├── Colo829-19_S4-sort.bam.bai │ ├── Colo829.18.chr20.MissedStrongLoh.bam │ ├── Colo829.18.chr20.MissedStrongLoh.bam.bai │ ├── Colo829.19.chr20.MissedStrongLoh.bam │ ├── Colo829.19.chr20.MissedStrongLoh.bam.bai │ ├── Colo829.chr10.CandDel5.bam │ ├── Colo829.chr10.CandDel5.bam.bai │ ├── Colo829.chr10.DELDiscReverse.bam │ ├── Colo829.chr10.DELDiscReverse.bam.bai │ ├── Colo829.chr10.LGDEL3.bam │ ├── Colo829.chr10.LGDEL3.bam.bai │ ├── Colo829.chr10.LGINS30.bam │ ├── Colo829.chr10.LGINS30.bam.bai │ ├── Colo829.chr20.CRISPR.bam │ ├── Colo829.chr20.CRISPR.bam.bai │ ├── Colo829.chr20.CandDel5SV.bam │ ├── Colo829.chr20.CandDel5SV.bam.bai │ ├── Colo829.chr20.DEL.bam │ ├── Colo829.chr20.DEL.bam.bai │ ├── Colo829.chr20.DELSV3Happy.bam │ ├── Colo829.chr20.DELSV3Happy.bam.bai │ ├── Colo829.chr20.DELSV3Unhappy.bam │ ├── Colo829.chr20.DELSV3Unhappy.bam.bai │ ├── Colo829.chr20.DELSV5Happy.bam │ ├── Colo829.chr20.DELSV5Happy.bam.bai │ ├── Colo829.chr20.DUPDiscSV.bam │ ├── Colo829.chr20.DUPDiscSV.bam.bai │ ├── Colo829.chr20.INVSV.bam │ ├── Colo829.chr20.INVSV.bam.bai │ ├── Colo829.chr20.MarkingDUPSV.bam │ ├── Colo829.chr20.MarkingDUPSV.bam.bai │ ├── Colo829.chr20.OverlapSV.bam │ ├── Colo829.chr20.OverlapSV.bam.bai │ ├── Colo829.chr20.SVBP.bam │ ├── Colo829.chr20.SVBP.bam.bai │ ├── Colo829.chr20.SVBPReverse.bam │ ├── Colo829.chr20.SVBPReverse.bam.bai │ ├── Count-Depth-With-Ns.bam │ ├── Count-Depth-With-Ns.bam.bai │ ├── DELDiscPairRreference.bam │ ├── DELDiscPairRreference.bam.bai │ ├── DelOutOfBound.chr1_150578117_150578617.bam │ ├── DelOutOfBound.chr1_150578117_150578617.bam.bai │ ├── ExtraSVInRealignment.chr1_11144571_11144831.bam │ ├── ExtraSVInRealignment.chr1_11144571_11144831.bam.bai │ ├── HCC2218_BL_realigins.bam │ ├── HCC2218_BL_realigins.bam.bai │ ├── HCC2218_C_position_bug.bam │ ├── HCC2218_C_position_bug.bam.bai │ ├── HCC2218_C_realigins.bam │ ├── HCC2218_C_realigins.bam.bai │ ├── HardClipInSV.S2.clipped.bam │ ├── HardClipInSV.S2.clipped.bam.bai │ ├── L861Q.bam │ ├── L861Q.bam.bai │ ├── MRE11a.bam │ ├── MRE11a.bam.bai │ ├── N13532.TwoDels1InsStringBoundError.bam │ ├── N13532.TwoDels1InsStringBoundError.bam.bai │ ├── NA12878.chr6_137219200-137219700.bam │ ├── NA12878.chr6_137219200-137219700.bam.bai │ ├── NA12878.chrom20.DELSV.bam │ ├── NA12878.chrom20.DELSV.bam.bai │ ├── NA12878.chrom20.INVFullSV.bam │ ├── NA12878.chrom20.INVFullSV.bam.bai │ ├── NA12878.chrom20.INVSimpleSV.bam │ ├── NA12878.chrom20.INVSimpleSV.bam.bai │ ├── NA12878.chrom20.StrSomSamSpec.bam │ ├── NA12878.chrom20.StrSomSamSpec.bam.bai │ ├── NA12878.chrom20.Unmapped.reads.bam │ ├── NA12878.chrom20.Unmapped.reads.bam.bai │ ├── NA12878.chrom5.DUPSV.140594296-140594495.bam │ ├── NA12878.chrom5.DUPSV.140594296-140594495.bam.bai │ ├── NA12878.part1.1956957-1957177.bam │ ├── NA12878.part1.1956957-1957177.bam.bai │ ├── NA12889.chrom20.StrSomSamSpec.bam │ ├── NA12889.chrom20.StrSomSamSpec.bam.bai │ ├── NA12889.part1.1956957-1957177.bam │ ├── NA12889.part1.1956957-1957177.bam.bai │ ├── NA21144.chrom11.DUPDiscF.bam │ ├── NA21144.chrom11.DUPDiscF.bam.bai │ ├── NA21144.chrom11.Duplicates.bam │ ├── NA21144.chrom11.Duplicates.bam.bai │ ├── NA21144.chrom11.INV3Disc.bam │ ├── NA21144.chrom11.INV3Disc.bam.bai │ ├── NA21144.chrom11.INV5Disc.bam │ ├── NA21144.chrom11.INV5Disc.bam.bai │ ├── NA24385.REF.SVDEL.bam │ ├── NA24385.REF.SVDEL.bam.bai │ ├── NA24385_Insertion_chr20_60465664_60468868.bam │ ├── NA24385_Insertion_chr20_60465664_60468868.bam.bai │ ├── NA24385_chr_19_58559581_58567861.bam │ ├── NA24385_chr_19_58559581_58567861.bam.bai │ ├── NA24385_chr_1_246981051_246981611.bam │ ├── NA24385_chr_1_246981051_246981611.bam.bai │ ├── NA24385_chr_20_18783981_18855722.bam │ ├── NA24385_chr_20_18783981_18855722.bam.bai │ ├── NA24385_chr_20_20156208_20234556.bam │ ├── NA24385_chr_20_20156208_20234556.bam.bai │ ├── NA24385_chr_20_20525032_20604921.bam │ ├── NA24385_chr_20_20525032_20604921.bam.bai │ ├── NA24385_chr_20_36018823_36039513.bam │ ├── NA24385_chr_20_36018823_36039513.bam.bai │ ├── NA24385_chr_20_38386265_38409801.bam │ ├── NA24385_chr_20_38386265_38409801.bam.bai │ ├── NA24385_chr_20_44885701_44969115.bam │ ├── NA24385_chr_20_44885701_44969115.bam.bai │ ├── NA24385_cnt0.bam │ ├── NA24385_cnt0.bam.bai │ ├── NA24385_tcov_empty.bam │ ├── NA24385_tcov_empty.bam.bai │ ├── NA24631_sorted.chr1.1000k.bam │ ├── NA24631_sorted.chr1.1000k.bam.bai │ ├── NAP1L1.NegativeRRC.bam │ ├── NAP1L1.NegativeRRC.bam.bai │ ├── NPE_NM_JOIN_Normal.bam │ ├── NPE_NM_JOIN_Normal.bam.bai │ ├── NPE_NM_JOIN_Tumor.bam │ ├── NPE_NM_JOIN_Tumor.bam.bai │ ├── NPE_insertion_adjust_ref.bam │ ├── NPE_insertion_adjust_ref.bam.bai │ ├── NPE_tcov_toVars.bam │ ├── NPE_tcov_toVars.bam.bai │ ├── NormalA.StrongLOH.chr21.bam │ ├── NormalA.StrongLOH.chr21.bam.bai │ ├── T7-75_S10_chr10_DEL.bam │ ├── T7-75_S10_chr10_DEL.bam.bai │ ├── Tcov_zero_SV_DEL_candidate3.bam │ ├── Tcov_zero_SV_DEL_candidate3.bam.bai │ ├── TumorA.StrongLOH.chr21.bam │ ├── TumorA.StrongLOH.chr21.bam.bai │ ├── Zero_in_DUPSV_NORMAL.bam │ ├── Zero_in_DUPSV_NORMAL.bam.bai │ ├── Zero_in_DUPSV_TUMOUR.bam │ ├── Zero_in_DUPSV_TUMOUR.bam.bai │ ├── amp_allele_ins_repr.bam │ ├── amp_allele_ins_repr.bam.bai │ ├── beds │ ├── correct_5columns.bed │ ├── correct_8columns_amplicon.bed │ ├── correct_8columns_not_amplicon.bed │ ├── correct_9columns.bed │ ├── incorrect_4columns.bed │ └── incorrect_8columns.bed │ ├── hard_clip_next_to_del_test1.bam │ ├── hard_clip_next_to_del_test1.bam.bai │ ├── hard_clip_next_to_del_test2.bam │ ├── hard_clip_next_to_del_test2.bam.bai │ ├── invalid-char.bam │ ├── invalid-char.bam.bai │ ├── norealign-stringindex-oob.bam │ ├── norealign-stringindex-oob.bam.bai │ ├── short_quality_seq_in_sv.bam │ ├── short_quality_seq_in_sv.bam.bai │ ├── test-malformed-cigar-and-string-eor.bam │ ├── test-malformed-cigar-and-string-eor.bam.bai │ ├── test_alt_alleles.bam │ ├── test_alt_alleles.bam.bai │ ├── test_reads.hardclipped.bam │ ├── test_reads.hardclipped.bam.bai │ ├── threeIndels_zero_deletion_normal.bam │ ├── threeIndels_zero_deletion_normal.bam.bai │ ├── threeIndels_zero_deletion_tumor.bam │ └── threeIndels_zero_deletion_tumor.bam.bai ├── testdata ├── fastas │ ├── GRCh37.fa.csv │ ├── hard_clip_case.fa.csv │ ├── hg19.fa.csv │ ├── hg1k.fa.csv │ ├── hg38.fa.csv │ ├── hs37d5.fa.csv │ ├── hs38DH.fa.csv │ ├── mm10.fa.csv │ └── test.fa.csv └── integrationtestcases │ ├── Amplicon;GRCh37.fa;MRE11a.bam;chr11;94153228-94153388;94153261-94153357;-a 100.95 -p;.txt │ ├── Amplicon;hg19.fa;Colo829-18_S3-sort.bam;chr1;933866-934466;933866-934466;-a 100.95 -D;.txt │ ├── Simple;GRCh37.fa;HCC2218_C_position_bug.bam;chr2;179260451-179260596;-f 0.001.txt │ ├── Simple;GRCh37.fa;N13532.TwoDels1InsStringBoundError.bam;chr11;1280138-1280341;-f0.0025-F0x700-Q10.txt │ ├── Simple;GRCh37.fa;NA24385.REF.SVDEL.bam;chr1;9011935-9017839;-f 0.001.txt │ ├── Simple;GRCh37.fa;NA24385_Insertion_chr20_60464465_60470068.bam;chr20;60464465-60470068;-f 0.001.txt │ ├── Simple;GRCh37.fa;NA24385_chr_19_58559581-58567861.bam;chr20;58559581;58567861;-f0.001.txt │ ├── Simple;GRCh37.fa;NA24385_chr_20_20156208-20234556.bam;chr20;20156208;20234556;-f0.001-fisher.txt │ ├── Simple;GRCh37.fa;NA24385_chr_20_20156208-20234556.bam;chr20;20156208;20234556;-f0.001.txt │ ├── Simple;GRCh37.fa;NA24385_chr_20_36018823-36039513.bam;chr20;36018823;36039513;-f0.001.txt │ ├── Simple;GRCh37.fa;NA24385_chr_20_38386265-38409801.bam;chr20;38386265;38409801;-f0.001.txt │ ├── Simple;GRCh37.fa;NA24385_chr_20_44885701_44969115.bam;chr20;44885701;44969115;-f0.001.txt │ ├── Simple;GRCh37.fa;NA24385_cnt0.bam;chr11;3379106-3382196;-f 0.001.txt │ ├── Simple;GRCh37.fa;NA24385_tcov_empty.bam;chr8;122660146-122660347;-f 0.001.txt │ ├── Simple;GRCh37.fa;NA24631_sorted.chr1.1000k.bam;chr1;1;499702;-f0.001.txt │ ├── Simple;GRCh37.fa;NPE_insertion_adjust_ref.bam;chr3;145521599-145521750;-f 0.1--nosv--deldupvar-Q10-F0x700.txt │ ├── Simple;GRCh37.fa;short_quality_seq_in_sv.bam;chr1;17420079-17420230;-f 0.001.txt │ ├── Simple;hard_clip_case.fa;hard_clip_next_to_del_test1.bam;test;6674-6824;-f 0.0 -p -r 1.txt │ ├── Simple;hard_clip_case.fa;hard_clip_next_to_del_test2.bam;test;6434-6564;-f 0.0 -p -r 1.txt │ ├── Simple;hard_clip_case.fa;test_reads.hardclipped.bam;example_genome;160-280;-f 0.0 -P 0.txt │ ├── Simple;hg19.fa;Colo829-18_S3-sort.bam;chr1;9922-10122;--chimeric -p;.txt │ ├── Simple;hg19.fa;Colo829-18_S3-sort.bam;chr1;9922-10122;-p;.txt │ ├── Simple;hg19.fa;Colo829-18_S3-sort_chrY.bam;chrY;59016100-59016124;--chimeric -f 0.001.txt │ ├── Simple;hg19.fa;Colo829-18_S3-sort_chrY.bam;chrY;59016100-59016124;-f 0.001.txt │ ├── Simple;hg19.fa;Colo829.chr10.CandDel5.bam;chr10;134535815-134569759;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr10.DELDiscReverse.bam;chr10;89712340-89713976;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr10.LGDEL3.bam;chr10;127187158-127201055;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr10.LGINS30.bam;chr10;127800917-127802207;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.CRISPR.bam;chr20;50454281-50455444;-f 0.001 -J 50454941 -j 25;.txt │ ├── Simple;hg19.fa;Colo829.chr20.CandDel5SV.bam;chr20;506503-507295;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.DEL.bam;chr20;2802740-2803167;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.DELSV3Happy.bam;chr20;5023101-5026046;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.DELSV3Unhappy.bam;chr20;54440610-54441423;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.DELSV5Happy.bam;chr20;3097973-3098634;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.DUPDiscSV.bam;chr20;47124929-47131802;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.INVSV.bam;chr20;46841555-46845755;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.MarkingDUPSV.bam;chr20;47131954-47132045;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.OverlapSV.bam;chr20;31260388-31262431;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.SVBP.bam;chr20;3251475-3252255;-f 0.001;.txt │ ├── Simple;hg19.fa;Colo829.chr20.SVBPReverse.bam;chr20;318511-318527;-f 0.001;.txt │ ├── Simple;hg19.fa;HardClipInSV.S2.clipped.bam;chr7;1855769-1856455;-f 0.001;.txt │ ├── Simple;hg19.fa;L861Q.bam;chr7;55259400-55259600;-UN.txt │ ├── Simple;hg19.fa;L861Q.bam;chr7;55259400-55259600;-u.txt │ ├── Simple;hg19.fa;L861Q.bam;chr7;55259400-55259600;.txt │ ├── Simple;hg38.fa;2-364738.chr21.Negative.bam;chr21;28366637-28367427;-f0.01-Q10-F0x700.txt │ ├── Simple;hg38.fa;2-420233.chr7.Negative.bam;chr7;157482463-157483329;-f0.01-Q10-F0x700.txt │ ├── Simple;hg38.fa;AMP_allele.bam;chr19;19542710-19542720;-f0.0.txt │ ├── Simple;hg38.fa;CIGAR_Three_Indels_DLEN.bam;chr9;107331700-107331701;-f0.001.txt │ ├── Simple;hg38.fa;DELDiscPairRreference.bam;chr1;43894440-43894460;-f 0.001.txt │ ├── Simple;hg38.fa;DelOutOfBound.bam;chr1;150578117-150578617;-f0.001--deldupvar.txt │ ├── Simple;hg38.fa;DelOutOfBound.bam;chr1;150578117-150578617;-f0.001.txt │ ├── Simple;hg38.fa;ExtraSVInRealignment.bam;chr1;11144571-11144831;-f 0.001-U.txt │ ├── Simple;hg38.fa;ExtraSVInRealignment.bam;chr1;11144571-11144831;-f 0.001.txt │ ├── Simple;hg38.fa;NA12878.bam;chr6;137219200-137219700;-f0.001-Q10-F0x700.txt │ ├── Simple;hg38.fa;NAP1L1.NegativeRRC.bam;chr12;76036587-76085033;-f 0.001.txt │ ├── Simple;hg38.fa;NPE_tcov_toVars.bam;chr7;140453040;140479569;-f 0.1.txt │ ├── Simple;hg38.fa;Tcov_zero_SV_DEL_candidate3.bam;chr8;90534611;90620070;-f 0.1 -i.txt │ ├── Simple;hg38.fa;Tcov_zero_SV_DEL_candidate3.bam;chr8;90534611;90620070;-f 0.1.txt │ ├── Simple;hg38.fa;invalid-char.bam;chr9;107331070-107331095;-f0.001.txt │ ├── Simple;hg38.fa;norealign-stringindex-oob.bam;chr22;20566544;20566545;-f 0.001-k0.txt │ ├── Simple;hg38.fa;test-malformed-cigar-and-string-eor.bam;chr4;25001600-25001607;-f0.001.txt │ ├── Simple;hs37d5.fa;NA21144.chrom11.Duplicates.bam;11;402283-410793;-F 0;.txt │ ├── Simple;hs37d5.fa;NA21144.chrom11.Duplicates.bam;11;402283-410793;.txt │ ├── Simple;hs38DH.fa;Count-Depth-With-Ns.bam;chr1;391310-391333;-K -p -r 1 -q 2 -f 0.0;.txt │ ├── Simple;hs38DH.fa;Count-Depth-With-Ns.bam;chr1;391310-391333;-p -r 1 -q 2 -f 0.0;.txt │ ├── Simple;hs38DH.fa;NA12878.chrom20.DELSV.bam;chr20;62596000-62598000;-f 0.001.txt │ ├── Simple;hs38DH.fa;NA12878.chrom20.INVFullSV.bam;chr20;5927052-5927179;-f 0.001.txt │ ├── Simple;hs38DH.fa;NA12878.chrom20.INVSimpleSV.bam;chr20;1961100-1961400;-f 0.001.txt │ ├── Simple;hs38DH.fa;NA12878.chrom20.Unmapped.reads.bam;chr20;62597650-62597750;-q 20.txt │ ├── Simple;hs38DH.fa;NA12878.chrom5.DUPSV.bam;chr5;140594296-140594495;-f0.001.txt │ ├── Simple;hs38DH.fa;NA21144.chrom11.DUPDiscF.bam;chr11;77614410-77614671;-f 0.001.txt │ ├── Simple;hs38DH.fa;NA21144.chrom11.INV3Disc.bam;chr11;57982617-57982816;-f 0.001.txt │ ├── Simple;hs38DH.fa;NA21144.chrom11.INV5Disc.bam;chr11;57970876-57971275;-f 0.001.txt │ ├── Simple;mm10.fa;T7-75_S10_chr10_DEL.bam;chr10;11291400-11295220;-f 0.001;.txt │ ├── Simple;mm10.fa;T7-75_S10_chr10_DEL.bam;chr10;11291400-11295300;-f 0.001;.txt │ ├── Simple;test.fa;amp_allele_ins_repr.bam;test;148-149;-f 0.0 -p.txt │ ├── Simple;test.fa;test_alt_alleles.bam;chrT;0-52;-p.txt │ ├── Somatic;GRCh37.fa;NPE_NM_Tumor.bam-NPE_NM_Normal.bam;chr5;19375000-19376500;-f0.1--nosv--deldupvar-Q10-F0x700;.txt │ ├── Somatic;GRCh37.fa;NPE_NM_Tumor.bam-NPE_NM_Normal.bam;chr5;19375000-19376500;-f0.1-Q10-F0x700;.txt │ ├── Somatic;GRCh37.fa;threeIndels_zero_deletion_tumor.bam-threeIndels_zero_deletion_normal.bam;chr20;62354864-62374864;-f0.1-Q10-F0x700;.txt │ ├── Somatic;hg19.fa;ArgumentNA_Tumor.bam-ArgumentNA_Normal.bam;chr7;140453010-140453158;-q25-F0x100-f0.001-k1-M20-p-fisher;.txt │ ├── Somatic;hg19.fa;ArgumentNA_Tumor.bam-ArgumentNA_Normal.bam;chr7;140453010-140453158;-q25-F0x100-f0.001-k1-M20-p;.txt │ ├── Somatic;hg19.fa;Colo829-18_S3-sort.bam-Colo829-19_S4-sort.bam;chr10;1368753-1369353;.txt │ ├── Somatic;hg19.fa;Colo829-18_S3-sort.bam-Colo829-19_S4-sort.bam;chr10;684892-685492;.txt │ ├── Somatic;hg19.fa;Colo829-18_S3-sort.bam-Colo829-19_S4-sort.bam;chr1;755917-756517;.txt │ ├── Somatic;hg19.fa;Colo829.18.chr20.MissedStrongLoh.bam-Colo829.19.chr20.MissedStrongLoh.bam;chr20;59844695;59857589;-f0.001.txt │ ├── Somatic;hg19.fa;HCC2218_BL_realigins.bam-HCC2218_C_realigins.bam;chrX;7811670-7811868;-f0.001;.txt │ ├── Somatic;hg19.fa;Zero_in_DUPSV_TUMOUR.bam-Zero_in_DUPSV_NORMAL.bam;chr19;290742-291636;-f0.001-X3.txt │ ├── Somatic;hg1k.fa;TumorA.StrongLOH.bam-NormalA.StrongLOH.bam;chr21;10996701-11186054;-Q10-f0.01-r2-V0.05;.txt │ ├── Somatic;hs37d5.fa;NA12878.part1.1956957-1957177.bam-NA12889.part1.1956957-1957177.bam;chr1;1956957-1957177;-f0.001;.txt │ ├── Somatic;hs38DH.fa;172T_S8.final.chr1.bam-172N_S7.final.chr1.bam;chr1;11182030-11182188;;.txt │ └── Somatic;hs38DH.fa;NA12889.StrSomSamSpec.bam-NA12878.StrSomSamSpec.bam;chr20;43246926-43280248;-f0.001.txt └── tests └── integration ├── config.sh ├── expected ├── vardict.paired.vcf └── vardict.simple.vcf ├── non_deterministic_behavior ├── Colo829.chr20.PerlNonDeterm.bam └── Colo829.chr20.PerlNonDeterm.bam.bai ├── raw_input ├── raw.vardict.paired.var └── raw.vardict.simple.var ├── test_non_deterministic_behavior.out ├── test_non_deterministic_behavior.sh ├── tests_integration.sh └── vardictColo20_1.perl.txt /.gitignore: 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