├── .cliff.toml ├── .gitattributes ├── .github ├── CODEOWNERS ├── FUNDING.yml ├── actions │ └── docs │ │ └── action.yaml ├── logos │ ├── fulcrumgenomics.svg │ ├── idtdna.png │ ├── igenomx.png │ ├── jumpcodegenomics.png │ ├── missionbio.svg │ ├── myriad.png │ ├── singulargenomics.svg │ ├── strataoncology.png │ ├── twinstrandbio.svg │ └── verogen.jpg └── workflows │ ├── release.yaml │ └── unittests.yaml ├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── codecov.yml ├── docs ├── FastqToConsensus-RnD.smk └── best-practice-consensus-pipeline.md ├── project ├── build.properties └── plugins.sbt ├── run_metrics_doclet.sh ├── src ├── main │ ├── java │ │ └── com │ │ │ └── fulcrumgenomics │ │ │ └── util │ │ │ ├── DnaFoldPrediction.java │ │ │ ├── DnaFoldPredictor.java │ │ │ ├── PickIlluminaIndicesCommand.java │ │ │ └── PickLongIndices.scala │ ├── resources │ │ ├── com │ │ │ └── fulcrumgenomics │ │ │ │ ├── bam │ │ │ │ ├── ErrorRateByReadPosition.R │ │ │ │ └── FindSwitchbackReads.R │ │ │ │ ├── rnaseq │ │ │ │ ├── CollectErccMetrics.R │ │ │ │ └── ErccStandardMixtures.txt │ │ │ │ └── umi │ │ │ │ └── CollectDuplexSeqMetrics.R │ │ └── log4j2.xml │ └── scala │ │ └── com │ │ └── fulcrumgenomics │ │ ├── FgBioDef.scala │ │ ├── alignment │ │ ├── Aligner.scala │ │ ├── Alignment.scala │ │ └── Matrix.scala │ │ ├── bam │ │ ├── AutoGenerateReadGroupsByName.scala │ │ ├── Bams.scala │ │ ├── BaseCounts.scala │ │ ├── CallOverlappingConsensusBases.scala │ │ ├── ClipBam.scala │ │ ├── DownsampleAndNormalizeBam.scala │ │ ├── ErrorRateByReadPosition.scala │ │ ├── EstimatePoolingFractions.scala │ │ ├── FilterBam.scala │ │ ├── FindSwitchbackReads.scala │ │ ├── FindTechnicalReads.scala │ │ ├── OverlappingBasesConsensusCaller.scala │ │ ├── RandomizeBam.scala │ │ ├── ReadAndRefPosIterator.scala │ │ ├── RemoveSamTags.scala │ │ ├── SamRecordClipper.scala │ │ ├── SetMateInformation.scala │ │ ├── SortBam.scala │ │ ├── SplitBam.scala │ │ ├── TrimPrimers.scala │ │ ├── UpdateReadGroups.scala │ │ ├── ZipperBams.scala │ │ ├── api │ │ │ ├── HeaderHelper.scala │ │ │ ├── SamIterator.scala │ │ │ ├── SamOrder.scala │ │ │ ├── SamRecord.scala │ │ │ ├── SamRecordCodec.scala │ │ │ ├── SamSource.scala │ │ │ └── SamWriter.scala │ │ └── pileup │ │ │ ├── Pileup.scala │ │ │ ├── PileupBuilder.scala │ │ │ ├── RandomAccessPileupBuilder.scala │ │ │ └── StreamingPileupBuilder.scala │ │ ├── basecalling │ │ ├── ExtractBasecallingParamsForPicard.scala │ │ └── ExtractIlluminaRunInfo.scala │ │ ├── cmdline │ │ ├── ClpGroups.scala │ │ ├── FgBioMain.scala │ │ └── FgBioTool.scala │ │ ├── coord │ │ └── LocatableOrdering.scala │ │ ├── fasta │ │ ├── CollectAlternateContigNames.scala │ │ ├── HardMaskFasta.scala │ │ ├── ReferenceSequenceIterator.scala │ │ ├── SequenceDictionary.scala │ │ ├── SortSequenceDictionary.scala │ │ └── UpdateFastaContigNames.scala │ │ ├── fastq │ │ ├── DemuxFastqs.scala │ │ ├── FastqRecord.scala │ │ ├── FastqSource.scala │ │ ├── FastqToBam.scala │ │ ├── FastqWriter.scala │ │ ├── QualityEncoding.scala │ │ ├── SortFastq.scala │ │ └── TrimFastq.scala │ │ ├── illumina │ │ ├── RunInfo.scala │ │ ├── Sample.scala │ │ └── SampleSheet.scala │ │ ├── internal │ │ ├── BuildToolDocs.scala │ │ ├── FgMetricsDoclet.scala │ │ └── InternalTools.scala │ │ ├── math │ │ ├── BinomialDistribution.scala │ │ └── FishersExactTest.scala │ │ ├── personal │ │ ├── nhomer │ │ │ ├── GenerateRegionsFromFasta.scala │ │ │ └── SplitTag.scala │ │ └── tfenne │ │ │ ├── StripFastqReadNumbers.scala │ │ │ └── SummarizeGff.scala │ │ ├── rnaseq │ │ ├── CollectErccMetrics.scala │ │ └── EstimateRnaSeqInsertSize.scala │ │ ├── testing │ │ ├── ReferenceSetBuilder.scala │ │ ├── SamBuilder.scala │ │ ├── VariantContextSetBuilder.scala │ │ └── VcfBuilder.scala │ │ ├── umi │ │ ├── AnnotateBamWithUmis.scala │ │ ├── CallCodecConsensusReads.scala │ │ ├── CallDuplexConsensusReads.scala │ │ ├── CallMolecularConsensusReads.scala │ │ ├── CodecConsensusCaller.scala │ │ ├── CollectDuplexSeqMetrics.scala │ │ ├── ConsensusCaller.scala │ │ ├── ConsensusCallingIterator.scala │ │ ├── ConsensusTags.scala │ │ ├── CopyUmiFromReadName.scala │ │ ├── CorrectUmis.scala │ │ ├── DuplexConsensusCaller.scala │ │ ├── ExtractUmisFromBam.scala │ │ ├── FilterConsensusReads.scala │ │ ├── GroupReadsByUmi.scala │ │ ├── ReviewConsensusVariants.scala │ │ ├── SimpleConsensusCaller.scala │ │ ├── UmiConsensusCaller.scala │ │ ├── Umis.scala │ │ └── VanillaUmiConsensusCaller.scala │ │ ├── util │ │ ├── Amplicon.scala │ │ ├── AmpliconDetector.scala │ │ ├── AssignPrimers.scala │ │ ├── GeneAnnotations.scala │ │ ├── GenomicSpan.scala │ │ ├── IlluminaAdapters.scala │ │ ├── IntervalListSource.scala │ │ ├── IntervalListWriter.scala │ │ ├── Io.scala │ │ ├── MathUtil.scala │ │ ├── Metric.scala │ │ ├── MetricBuilder.scala │ │ ├── MetricSorter.scala │ │ ├── NcbiRefSeqGffSource.scala │ │ ├── NumericTypes.scala │ │ ├── PickIlluminaIndices.scala │ │ ├── ProgressLogger.scala │ │ ├── ReadStructure.scala │ │ ├── RefFlatSource.scala │ │ ├── Rscript.scala │ │ ├── SampleBarcodeMetric.scala │ │ ├── Sequences.scala │ │ ├── Sorter.scala │ │ ├── UpdateDelimitedFileContigNames.scala │ │ ├── UpdateGffContigNames.scala │ │ └── UpdateIntervalListContigNames.scala │ │ └── vcf │ │ ├── AssessPhasing.scala │ │ ├── ByIntervalListVariantContextIterator.scala │ │ ├── DownsampleVcf.scala │ │ ├── FixVcfPhaseSet.scala │ │ ├── HapCutToVcf.scala │ │ ├── JointVariantContextIterator.scala │ │ ├── MakeMixtureVcf.scala │ │ ├── MakeTwoSampleMixtureVcf.scala │ │ ├── UpdateVcfContigNames.scala │ │ ├── VariantMask.scala │ │ ├── api │ │ ├── Allele.scala │ │ ├── AlleleSet.scala │ │ ├── ArrayAttr.scala │ │ ├── Genotype.scala │ │ ├── GenotypeMap.scala │ │ ├── Variant.scala │ │ ├── VcfConversions.scala │ │ ├── VcfHeader.scala │ │ ├── VcfSource.scala │ │ └── VcfWriter.scala │ │ └── filtration │ │ ├── FilterSomaticVcf.scala │ │ ├── ReadEndSomaticVariantFilter.scala │ │ └── SomaticVariantFilter.scala └── test │ ├── resources │ └── com │ │ └── fulcrumgenomics │ │ ├── bam │ │ ├── 200reads.bam │ │ ├── error_rate_by_read_position.dict │ │ ├── error_rate_by_read_position.fasta.fai │ │ ├── estimate_pooling_fractions │ │ │ ├── HG01112.bai │ │ │ ├── HG01112.bam │ │ │ ├── HG01500.bai │ │ │ ├── HG01500.bam │ │ │ ├── HG01583.bai │ │ │ ├── HG01583.bam │ │ │ ├── HG01879.bai │ │ │ ├── HG01879.bam │ │ │ ├── HG03052.bai │ │ │ ├── HG03052.bam │ │ │ ├── HG03742.bai │ │ │ ├── HG03742.bam │ │ │ ├── regions.interval_list │ │ │ ├── variants.vcf.gz │ │ │ └── variants.vcf.gz.tbi │ │ ├── set_mate_coordinatesorted.sam │ │ ├── set_mate_querygrouped.sam │ │ ├── set_mate_querysorted.sam │ │ ├── trim_primers_test.dict │ │ ├── trim_primers_test.fa │ │ └── trim_primers_test.fa.fai │ │ ├── fasta │ │ ├── GRCh37.p13.assembly_report.txt │ │ ├── GRCh38.p12.assembly_report.txt │ │ ├── soft-masked.fa │ │ └── soft-masked.fa.fai │ │ ├── umi │ │ ├── annotate_umis.fastq │ │ └── annotate_umis.sam │ │ ├── util │ │ ├── human.gff.gz │ │ ├── miseq │ │ │ ├── SampleSheet.csv │ │ │ ├── SampleSheet.lanes.csv │ │ │ ├── SampleSheetNoSampleSection.csv │ │ │ ├── SampleSheetOnlyRequired.csv │ │ │ └── SampleSheetSampleMissingColumns.csv │ │ └── refFlat.txt.gz │ │ └── vcf │ │ ├── testdata │ │ ├── NA12878.GIABPedigreev0.2.17.41100000.41300000.hapcut │ │ ├── NA12878.GIABPedigreev0.2.17.41100000.41300000.hapcut.gatk.vcf │ │ ├── NA12878.GIABPedigreev0.2.17.41100000.41300000.hapcut.vcf │ │ ├── NA12878.GIABPedigreev0.2.17.41100000.41300000.hapcut2 │ │ ├── NA12878.GIABPedigreev0.2.17.41100000.41300000.hapcut2.gatk.vcf │ │ ├── NA12878.GIABPedigreev0.2.17.41100000.41300000.hapcut2.vcf │ │ ├── NA12878.GIABPedigreev0.2.17.41100000.41300000.vcf │ │ ├── block_has_phased_genotypes.hapcut │ │ ├── blocks_out_of_order.hapcut2 │ │ ├── blocks_out_of_order.hapcut2.vcf │ │ ├── blocks_out_of_order.vcf │ │ ├── hapcut2_for_missing_genotype_info.vcf │ │ ├── intervalList.1-10.assess_phasing_metrics.block_lengths.txt │ │ ├── intervalList.1-10.assess_phasing_metrics.txt │ │ ├── intervalList.1-20.assess_phasing_metrics.block_lengths.txt │ │ ├── intervalList.1-20.assess_phasing_metrics.txt │ │ ├── intervalList.1-21.assess_phasing_metrics.block_lengths.txt │ │ ├── intervalList.1-21.assess_phasing_metrics.txt │ │ ├── intervalList.11-20.assess_phasing_metrics.block_lengths.txt │ │ ├── intervalList.11-20.assess_phasing_metrics.txt │ │ ├── intervalList.21-21.assess_phasing_metrics.block_lengths.txt │ │ ├── intervalList.21-21.assess_phasing_metrics.txt │ │ ├── intervalList.30-42.assess_phasing_metrics.block_lengths.txt │ │ ├── intervalList.30-42.assess_phasing_metrics.txt │ │ ├── missing_leading_variants.hapcut2 │ │ ├── missing_leading_variants.vcf │ │ ├── noIntervalList.1-10.assess_phasing.vcf.gz │ │ ├── noIntervalList.1-10.assess_phasing_metrics.block_lengths.txt │ │ ├── noIntervalList.1-10.assess_phasing_metrics.txt │ │ ├── noIntervalList.1-20.assess_phasing_metrics.block_lengths.txt │ │ ├── noIntervalList.1-20.assess_phasing_metrics.txt │ │ ├── noIntervalList.1-21.assess_phasing_metrics.block_lengths.txt │ │ ├── noIntervalList.1-21.assess_phasing_metrics.txt │ │ ├── noIntervalList.1-29.assess_phasing_metrics.block_lengths.txt │ │ ├── noIntervalList.1-29.assess_phasing_metrics.txt │ │ ├── noIntervalList.1-42.assess_phasing_metrics.block_lengths.txt │ │ ├── noIntervalList.1-42.assess_phasing_metrics.txt │ │ ├── noIntervalList.11-20.assess_phasing_metrics.block_lengths.txt │ │ ├── noIntervalList.11-20.assess_phasing_metrics.txt │ │ ├── noIntervalList.21-21.assess_phasing_metrics.block_lengths.txt │ │ ├── noIntervalList.21-21.assess_phasing_metrics.txt │ │ ├── noIntervalList.30-42.assess_phasing_metrics.block_lengths.txt │ │ ├── noIntervalList.30-42.assess_phasing_metrics.txt │ │ ├── no_switch_errors.hapcut2 │ │ ├── no_switch_errors.vcf │ │ ├── skip_prune.hapcut2 │ │ ├── skip_prune.vcf │ │ ├── with_iupac.hapcut │ │ ├── with_iupac.vcf │ │ ├── with_switch_errors.hapcut2 │ │ └── with_switch_errors.vcf │ │ └── update_vcf_contig_names │ │ ├── GRCh38.p12.dict │ │ └── hg38.dict │ └── scala │ └── com │ └── fulcrumgenomics │ ├── FgBioDefTest.scala │ ├── alignment │ ├── AlignerTest.scala │ ├── AlignmentTest.scala │ └── MatrixTest.scala │ ├── bam │ ├── AutoGenerateReadGroupsByNameTest.scala │ ├── BamsTest.scala │ ├── CallOverlappingConsensusBasesTest.scala │ ├── ClipBamTest.scala │ ├── DownsampleAndNormalizeBamTest.scala │ ├── ErrorRateByReadPositionTest.scala │ ├── EstimatePoolingFractionsTest.scala │ ├── FilterBamTest.scala │ ├── FindSwitchbackReadsTest.scala │ ├── FindTechnicalReadsTest.scala │ ├── OverlappingBasesConsensusCallerTest.scala │ ├── RandomizeBamTest.scala │ ├── ReadAndRefPosIteratorTest.scala │ ├── RemoveSamTagsTest.scala │ ├── SamRecordClipperTest.scala │ ├── SetMateInformationTest.scala │ ├── SplitBamTest.scala │ ├── TrimPrimersTest.scala │ ├── UpdateReadGroupsTest.scala │ ├── ZipperBamsTest.scala │ ├── api │ │ ├── SamIoTest.scala │ │ ├── SamOrderTest.scala │ │ └── SamRecordTest.scala │ └── pileup │ │ ├── PileupBuilderTest.scala │ │ ├── PileupTest.scala │ │ ├── RandomAccessPileupBuilderTest.scala │ │ └── StreamingPileupBuilderTest.scala │ ├── basecalling │ ├── ExtractBasecallingParamsForPicardTest.scala │ └── ExtractIlluminaRunInfoTest.scala │ ├── cmdline │ ├── ClpTests.scala │ ├── FgBioToolTest.scala │ └── IntelCompressionTest.scala │ ├── coord │ └── LocatableOrderingTest.scala │ ├── fasta │ ├── CollectAlternateContigNamesTest.scala │ ├── HardMaskFastaTest.scala │ ├── SequenceDictionaryTest.scala │ ├── SortSequenceDictionaryTest.scala │ └── UpdateFastaContigNamesTest.scala │ ├── fastq │ ├── DemuxFastqsTest.scala │ ├── FastqIoTest.scala │ ├── FastqToBamTest.scala │ ├── QualityEncodingTest.scala │ ├── SortFastqTest.scala │ └── TrimFastqTest.scala │ ├── illumina │ ├── RunInfoTest.scala │ ├── SampleSheetTest.scala │ └── SampleTest.scala │ ├── math │ ├── BinomialDistributionTest.scala │ └── FishersExactTestTest.scala │ ├── rnaseq │ ├── CollectErccMetricsTest.scala │ └── EstimateRnaSeqInsertSizeTest.scala │ ├── testing │ ├── ReferenceSetBuilderTest.scala │ ├── UnitSpec.scala │ └── VariantContextSetBuilderTest.scala │ ├── umi │ ├── AnnotateBamWithUmisTest.scala │ ├── CallCodecConsensusReadsTest.scala │ ├── CallDuplexConsensusReadsTest.scala │ ├── CallMolecularConsensusReadsTest.scala │ ├── CodecConsensusCallerTest.scala │ ├── CollectDuplexSeqMetricsTest.scala │ ├── ConsensusCallerTest.scala │ ├── CopyUmiFromReadNameTest.scala │ ├── CorrectUmisTest.scala │ ├── DuplexConsensusCallerTest.scala │ ├── DuplexConsensusCallingIntegrationTest.scala │ ├── ExtractUmisFromBamTest.scala │ ├── FilterConsensusReadsTest.scala │ ├── GroupReadsByUmiTest.scala │ ├── ReviewConsensusVariantsTest.scala │ ├── SimpleConsensusCallerTest.scala │ ├── UmiConsensusCallerTest.scala │ ├── UmisTest.scala │ └── VanillaUmiConsensusCallerTest.scala │ ├── util │ ├── AmpliconDetectorTest.scala │ ├── AmpliconTest.scala │ ├── AssignPrimersTest.scala │ ├── GeneAnnotationsTest.scala │ ├── IntervalListSourceTest.scala │ ├── IntervalListWriterTest.scala │ ├── IoTest.scala │ ├── MathUtilTest.scala │ ├── MetricBuilderTest.scala │ ├── MetricSorterTest.scala │ ├── MetricTest.scala │ ├── NcbiRefSeqGffSourceTest.scala │ ├── NumericTypesTest.scala │ ├── PickIlluminaIndicesTest.scala │ ├── PickLongIndicesTest.scala │ ├── ProgressLoggerTest.scala │ ├── ReadStructureTest.scala │ ├── RefFlatSourceTest.scala │ ├── SampleBarcodeMetricTest.scala │ ├── SequencesTest.scala │ ├── SorterTest.scala │ ├── UpdateContigNamesSpec.scala │ ├── UpdateDelimitedFileContigNamesTest.scala │ ├── UpdateGffContigNamesTest.scala │ └── UpdateIntervalListContigNamesTest.scala │ └── vcf │ ├── AssessPhasingTest.scala │ ├── ByIntervalListVariantContextIteratorTest.scala │ ├── DownsampleVcfTest.scala │ ├── FixVcfPhaseSetTest.scala │ ├── HapCutToVcfTest.scala │ ├── JointVariantContextIteratorTest.scala │ ├── MakeMixtureVcfTest.scala │ ├── MakeTwoSampleMixtureVcfTest.scala │ ├── UpdateVcfContigNamesTest.scala │ 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