├── .github └── workflows │ ├── ci.yml │ └── deploy.yml ├── .gitignore ├── CHANGES.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── KEYS ├── LICENSE.txt ├── LICENSE_header.txt ├── README.md ├── SUPPORT.md ├── adam-apis ├── pom.xml └── src │ ├── main │ └── scala │ │ └── org │ │ └── bdgenomics │ │ └── adam │ │ └── api │ │ ├── java │ │ ├── GenomicDatasetConverters.scala │ │ ├── GenomicRDDConverters.scala │ │ └── JavaADAMContext.scala │ │ └── python │ │ └── DataFrameConversionWrapper.scala │ └── test │ ├── java │ └── org │ │ └── bdgenomics │ │ └── adam │ │ └── api │ │ └── java │ │ ├── JavaADAMCoverageConduit.java │ │ ├── JavaADAMFeatureConduit.java │ │ ├── JavaADAMFragmentConduit.java │ │ ├── JavaADAMGenotypeConduit.java │ │ ├── JavaADAMReadConduit.java │ │ ├── JavaADAMSequenceConduit.java │ │ ├── JavaADAMSliceConduit.java │ │ └── JavaADAMVariantConduit.java │ ├── resources │ └── indexed_bams │ │ ├── sorted.bam │ │ └── sorted.bam.bai │ └── scala │ └── org │ └── bdgenomics │ └── adam │ └── api │ └── java │ └── JavaADAMContextSuite.scala ├── adam-assembly ├── pom.xml └── src │ └── main │ └── scala │ └── org │ └── bdgenomics │ └── adam │ └── assembly │ └── Assembly.scala ├── adam-cli ├── .gitignore ├── pom.xml └── src │ ├── main │ ├── java-templates │ │ └── org │ │ │ └── bdgenomics │ │ │ └── adam │ │ │ └── cli │ │ │ └── About.java │ └── scala │ │ └── org │ │ └── bdgenomics │ │ └── adam │ │ └── cli │ │ ├── ADAM2Fastq.scala │ │ ├── ADAMMain.scala │ │ ├── CountReadKmers.scala │ │ ├── CountSliceKmers.scala │ │ ├── Coverage.scala │ │ ├── CramArgs.scala │ │ ├── FileSystemUtils.scala │ │ ├── FlagStat.scala │ │ ├── MergeShards.scala │ │ ├── PrintADAM.scala │ │ ├── TransformAlignments.scala │ │ ├── TransformFeatures.scala │ │ ├── TransformFragments.scala │ │ ├── TransformGenotypes.scala │ │ ├── TransformSequences.scala │ │ ├── TransformSlices.scala │ │ ├── TransformVariants.scala │ │ └── View.scala │ └── test │ ├── resources │ ├── artificial.counts.txt │ ├── artificial.fa │ ├── artificial.fa.fai │ ├── bqsr1-r1.fq │ ├── bqsr1-r2.fq │ ├── bqsr1.sam │ ├── chr5.phyloP46way.trunc.wigFix │ ├── contigs.fa │ ├── flag-values.sam │ ├── gencode.v7.annotation.trunc10.bed │ ├── log4j.properties │ ├── small.vcf │ ├── sorted.bam │ ├── sorted.bam.bai │ ├── sorted.counts.txt │ ├── sorted.lex.vcf │ └── sorted.vcf │ └── scala │ └── org │ └── bdgenomics │ └── adam │ └── cli │ ├── ADAM2FastqSuite.scala │ ├── ADAMMainSuite.scala │ ├── AboutSuite.scala │ ├── CountReadKmersSuite.scala │ ├── CountSliceKmersSuite.scala │ ├── CoverageSuite.scala │ ├── MergeShardsSuite.scala │ ├── ParquetLister.scala │ ├── TransformAlignmentsSuite.scala │ ├── TransformFeaturesSuite.scala │ ├── TransformFragmentsSuite.scala │ ├── TransformGenotypesSuite.scala │ ├── TransformVariantsSuite.scala │ └── ViewSuite.scala ├── adam-codegen ├── pom.xml └── src │ └── main │ └── scala │ └── org │ └── bdgenomics │ └── adam │ └── codegen │ ├── DumpSchemasToProduct.scala │ ├── DumpSchemasToProjectionEnums.scala │ ├── Generator.scala │ └── ReflectSchema.scala ├── adam-core ├── .gitignore ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── bdgenomics │ │ │ └── adam │ │ │ └── io │ │ │ ├── FastqInputFormat.java │ │ │ ├── FastqRecordReader.java │ │ │ ├── InterleavedFastqInputFormat.java │ │ │ ├── ResettableCompressedSplitLineReader.java │ │ │ └── SingleFastqInputFormat.java │ └── scala │ │ └── org │ │ └── bdgenomics │ │ └── adam │ │ ├── algorithms │ │ ├── consensus │ │ │ ├── Consensus.scala │ │ │ ├── ConsensusGenerator.scala │ │ │ ├── ConsensusGeneratorFromKnowns.scala │ │ │ ├── ConsensusGeneratorFromReads.scala │ │ │ ├── ConsensusGeneratorFromSmithWaterman.scala │ │ │ ├── NormalizationUtils.scala │ │ │ └── UnionConsensusGenerator.scala │ │ └── smithwaterman │ │ │ ├── SmithWaterman.scala │ │ │ ├── SmithWatermanConstantGapScoring.scala │ │ │ └── SmithWatermanGapScoringFromFn.scala │ │ ├── converters │ │ ├── AlignmentConverter.scala │ │ ├── DefaultHeaderLines.scala │ │ ├── FastaConverters.scala │ │ ├── FastqRecordConverter.scala │ │ ├── FragmentConverter.scala │ │ ├── TranscriptEffectConverter.scala │ │ └── VariantContextConverter.scala │ │ ├── ds │ │ ├── ADAMContext.scala │ │ ├── ADAMParquetInputFormat.scala │ │ ├── ADAMSaveAnyArgs.scala │ │ ├── GenomeBins.scala │ │ ├── GenomicBroadcast.scala │ │ ├── GenomicDataset.scala │ │ ├── GenomicDatasetConversion.scala │ │ ├── GenomicPartitioners.scala │ │ ├── InFormatter.scala │ │ ├── OutFormatter.scala │ │ ├── ReferencePartitioner.scala │ │ ├── RegionJoin.scala │ │ ├── SAMHeaderWriter.scala │ │ ├── ShuffleRegionJoin.scala │ │ ├── TreeRegionJoin.scala │ │ ├── VCFHeaderUtils.scala │ │ ├── feature │ │ │ ├── BEDInFormatter.scala │ │ │ ├── BEDOutFormatter.scala │ │ │ ├── CoverageDataset.scala │ │ │ ├── FeatureDataset.scala │ │ │ ├── FeatureParser.scala │ │ │ ├── Features.scala │ │ │ ├── GFF3HeaderWriter.scala │ │ │ ├── GFF3InFormatter.scala │ │ │ ├── GFF3OutFormatter.scala │ │ │ ├── GTFInFormatter.scala │ │ │ ├── GTFOutFormatter.scala │ │ │ ├── NarrowPeakInFormatter.scala │ │ │ └── NarrowPeakOutFormatter.scala │ │ ├── fragment │ │ │ ├── FragmentDataset.scala │ │ │ ├── InterleavedFASTQInFormatter.scala │ │ │ ├── Tab5InFormatter.scala │ │ │ └── Tab6InFormatter.scala │ │ ├── read │ │ │ ├── ADAMBAMOutputFormat.scala │ │ │ ├── ADAMCRAMOutputFormat.scala │ │ │ ├── ADAMSAMOutputFormat.scala │ │ │ ├── AlignmentDataset.scala │ │ │ ├── AnySAMInFormatter.scala │ │ │ ├── AnySAMOutFormatter.scala │ │ │ ├── BAMInFormatter.scala │ │ │ ├── BinQualities.scala │ │ │ ├── FASTQInFormatter.scala │ │ │ ├── FlagStat.scala │ │ │ ├── MDTagging.scala │ │ │ ├── MarkDuplicates.scala │ │ │ ├── ReadDataset.scala │ │ │ ├── ReferencePositionPair.scala │ │ │ ├── RepairPartitions.scala │ │ │ ├── SAMInFormatter.scala │ │ │ ├── SingleReadBucket.scala │ │ │ ├── realignment │ │ │ │ ├── IndelRealignmentTarget.scala │ │ │ │ ├── ModPartitioner.scala │ │ │ │ ├── RealignIndels.scala │ │ │ │ └── RealignmentTargetFinder.scala │ │ │ └── recalibration │ │ │ │ ├── Aggregate.scala │ │ │ │ ├── BaseQualityRecalibration.scala │ │ │ │ ├── Covariate.scala │ │ │ │ ├── CovariateKey.scala │ │ │ │ ├── CovariateSpace.scala │ │ │ │ ├── CycleCovariate.scala │ │ │ │ ├── DinucCovariate.scala │ │ │ │ ├── Observation.scala │ │ │ │ ├── ObservationTable.scala │ │ │ │ ├── RecalibrationTable.scala │ │ │ │ └── Recalibrator.scala │ │ ├── sequence │ │ │ ├── FASTAInFormatter.scala │ │ │ ├── FlankSlices.scala │ │ │ ├── SequenceDataset.scala │ │ │ └── SliceDataset.scala │ │ └── variant │ │ │ ├── ADAMVCFOutputFormat.scala │ │ │ ├── GenotypeDataset.scala │ │ │ ├── VCFInFormatter.scala │ │ │ ├── VCFOutFormatter.scala │ │ │ ├── VariantContextDataset.scala │ │ │ └── VariantDataset.scala │ │ ├── models │ │ ├── Alphabet.scala │ │ ├── Attribute.scala │ │ ├── Coverage.scala │ │ ├── IndelTable.scala │ │ ├── MdTag.scala │ │ ├── NonoverlappingRegions.scala │ │ ├── ReadGroupDictionary.scala │ │ ├── ReferencePosition.scala │ │ ├── ReferenceRegion.scala │ │ ├── SAMFileHeaderWritable.scala │ │ ├── SequenceDictionary.scala │ │ ├── SnpTable.scala │ │ ├── VCFHeaderWritable.scala │ │ └── VariantContext.scala │ │ ├── projections │ │ ├── FieldEnumeration.scala │ │ └── Projection.scala │ │ ├── rich │ │ ├── RichAlignment.scala │ │ ├── RichCigar.scala │ │ └── RichVariant.scala │ │ ├── serialization │ │ └── ADAMKryoRegistrator.scala │ │ ├── sql │ │ └── VariantContext.scala │ │ └── util │ │ ├── ADAMShell.scala │ │ ├── ASCIITable.scala │ │ ├── AttributeUtils.scala │ │ ├── FileExtensions.scala │ │ ├── FileMerger.scala │ │ ├── GenomeFileReader.scala │ │ ├── IndexedFastaFile.scala │ │ ├── ManualRegionPartitioner.scala │ │ ├── ParallelFileMerger.scala │ │ ├── ParquetFileTraversable.scala │ │ ├── ParquetLogger.scala │ │ ├── PhredUtils.scala │ │ ├── ReferenceFile.scala │ │ ├── ReferenceMap.scala │ │ ├── SequenceDictionaryReader.scala │ │ ├── TextAlignment.scala │ │ ├── TextRddWriter.scala │ │ └── TwoBitFile.scala │ └── test │ ├── resources │ ├── HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_all.fixed-phase-set.excerpt.vcf │ ├── HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_all.fixed-phase-set.excerpt.vcf.README │ ├── HLA_DQB1_05_01_01_02.dict │ ├── HLA_DQB1_05_01_01_02.fa │ ├── HLA_DQB1_05_01_01_02.fa.fai │ ├── Homo_sapiens.GRCh37.75.trun100.gtf │ ├── Homo_sapiens.GRCh37.75.trun20.gtf │ ├── Hs_Ensembl_example_genes.gtf │ ├── NA12878.1_854950_855150.sam │ ├── NA12878.1_922305.G_GC_hom.sam │ ├── NA12878.chr22.tiny.freebayes.vcf │ ├── NA12878.sam │ ├── SeqCap_EZ_Exome_v3.hg19.interval_list │ ├── artificial.README.txt │ ├── artificial.cram │ ├── artificial.fa │ ├── artificial.fa.fai │ ├── artificial.realigned.sam │ ├── artificial.sam │ ├── badheader.sam │ ├── bams │ │ └── small.bam │ ├── bqsr1-r1.fq │ ├── bqsr1-r2.fq │ ├── bqsr1-ref.observed │ ├── bqsr1.sam │ ├── bqsr1.snps │ ├── bqsr1.vcf │ ├── bqsr1.vcf.tbi │ ├── chr20.250k.fa.gz │ ├── chromInfo.txt │ ├── combined_2018-05-18.9900-10050.fastq │ ├── ctg123.fasta.gff3 │ ├── dict_with_accession.dict │ ├── dvl1.200.bed │ ├── dvl1.200.gff3 │ ├── dvl1.200.gtf │ ├── env_test_command.sh │ ├── example_intervals.list │ ├── fastq_nobases.fq │ ├── fastq_noqual.fq │ ├── fastq_sample1.fq │ ├── fastq_sample1.fq.bgz │ ├── fastq_sample1.fq.bz2 │ ├── fastq_sample1.fq.gz │ ├── fastq_sample2.fq │ ├── fastq_sample3.fq │ ├── fastq_sample4.fq │ ├── fastq_to_usam.py │ ├── gencode.chr20.transcript_names.head10.txt │ ├── gencode.v19.annotation.chr20.250k.gtf │ ├── gencode.v19.pc_transcripts.250k.fa.gz │ ├── gencode.v7.annotation.trunc10.bed │ ├── gvcf_dir │ │ ├── gvcf_multiallelic.g.vcf │ │ └── gvcf_multiallelic_noPLs.g.vcf │ ├── gvcf_multiallelic │ │ └── multiallelic.vcf │ ├── hg19.chrM.2bit │ ├── hg19.genome │ ├── hg19.genome.txt │ ├── hs37d5.dict │ ├── hs38DH_chr1_10.fa │ ├── human_g1k_v37_chr1_59kb.2bit │ ├── human_g1k_v37_chr1_59kb.fasta │ ├── improper_pairs_1.fq │ ├── improper_pairs_2.fq │ ├── indexed_bams │ │ ├── sorted.2.bai │ │ ├── sorted.2.bam │ │ ├── sorted.bam │ │ └── sorted.bam.bai │ ├── inf_float_values.vcf │ ├── interleaved_fastq_sample1.ifq │ ├── interleaved_fastq_sample1.ifq.bgz │ ├── interleaved_fastq_sample1.ifq.bz2 │ ├── interleaved_fastq_sample1.ifq.gz │ ├── interleaved_fastq_sample1.ifq.output │ ├── interleaved_fastq_sample2.ifq │ ├── interleaved_fastq_sample2.ifq.output │ ├── interleaved_fastq_sample3.ifq │ ├── interleaved_fastq_sample3.ifq.output │ ├── interleaved_fastq_sample4.ifq │ ├── interleaved_fastq_sample4.ifq.output │ ├── interleaved_fastq_sample5.ifq │ ├── interleaved_fastq_sample5.ifq.output │ ├── invalid │ │ ├── small.INFO_flag.vcf │ │ └── truth_small_variants.vcf │ ├── legacy.fa │ ├── log4j.properties │ ├── multi_chr.sam │ ├── multiline_fastq.fq │ ├── nan_float_values.vcf │ ├── ordered.sam │ ├── proper_pairs_1.fq │ ├── proper_pairs_2.fq │ ├── queryname.sam │ ├── random.vcf │ ├── read_names_with_index_sequences_interleaved.fq │ ├── read_names_with_index_sequences_pair1.fq │ ├── read_names_with_index_sequences_pair2.fq │ ├── readname_sorted.sam │ ├── reads-0-2-0 │ ├── reads12.sam │ ├── reads12_diff1.sam │ ├── reads13.sam │ ├── reads21.sam │ ├── sample1.query.sam │ ├── sample1.queryname.sam │ ├── sample_coverage.bed │ ├── single_fastq_sample1.fq.output │ ├── single_fastq_sample2.fq.output │ ├── single_fastq_sample3.fq.output │ ├── single_fastq_sample4.fq.output │ ├── small.1.bed │ ├── small.1.narrowPeak │ ├── small.1.sam │ ├── small.1_12.bed │ ├── small.addctg.vcf │ ├── small.badheader.sam │ ├── small.sam │ ├── small.vcf │ ├── small_missing.vcf │ ├── small_realignment_targets.intervals │ ├── small_realignment_targets.pileup │ ├── small_realignment_targets.sam │ ├── small_realignment_targets_README.txt │ ├── small_snpeff.vcf │ ├── sorted-variants.lex.vcf │ ├── sorted-variants.vcf │ ├── sorted.lex.vcf │ ├── sorted.sam │ ├── sorted.vcf │ ├── tab5_to_usam.py │ ├── tab6_to_usam.py │ ├── tag.sam │ ├── tags.sam │ ├── test.compressed.bcf │ ├── test.conf │ ├── test.uncompressed.bcf │ ├── test.vcf │ ├── test.vcf.bgz │ ├── test.vcf.bgzf.gz │ ├── test.vcf.gz │ ├── test_command.sh │ ├── test_rowgroup_rangeindex.1.txt │ ├── timeout.py │ ├── trinity.fa │ ├── unmapped.sam │ ├── unordered.sam │ ├── unsorted.sam │ ├── vcf_dir │ │ ├── 1.vcf │ │ ├── 2.vcf │ │ ├── 3.vcf │ │ └── zero.vcf │ ├── wgEncodeOpenChromDnaseGm19238Pk.trunc10.narrowPeak │ └── wgs_calling_regions.hg38.interval_list │ └── scala │ └── org │ └── bdgenomics │ └── adam │ ├── algorithms │ ├── consensus │ │ ├── ConsensusGeneratorFromKnownsSuite.scala │ │ ├── ConsensusGeneratorFromReadsSuite.scala │ │ ├── ConsensusSuite.scala │ │ └── NormalizationUtilsSuite.scala │ └── smithwaterman │ │ └── SmithWatermanSuite.scala │ ├── converters │ ├── AlignmentConverterSuite.scala │ ├── FastqRecordConverterSuite.scala │ ├── FragmentConverterSuite.scala │ ├── TranscriptEffectConverterSuite.scala │ └── VariantContextConverterSuite.scala │ ├── ds │ ├── ADAMContextSuite.scala │ ├── GenomicDatasetSuite.scala │ ├── GenomicPositionPartitionerSuite.scala │ ├── InnerShuffleRegionJoinSuite.scala │ ├── InnerTreeRegionJoinSuite.scala │ ├── LeftOuterShuffleRegionJoinAndGroupByLeftSuite.scala │ ├── LeftOuterShuffleRegionJoinSuite.scala │ ├── OuterRegionJoinSuite.scala │ ├── RightOuterTreeRegionJoinSuite.scala │ ├── SortedGenomicDatasetSuite.scala │ ├── TreeRegionJoinSuite.scala │ ├── feature │ │ ├── CoverageDatasetSuite.scala │ │ ├── FeatureDatasetSuite.scala │ │ └── GFF3HeaderWriterSuite.scala │ ├── fragment │ │ └── FragmentDatasetSuite.scala │ ├── read │ │ ├── AlignmentDatasetSuite.scala │ │ ├── BinQualitiesSuite.scala │ │ ├── FlagStatSuite.scala │ │ ├── MDTaggingSuite.scala │ │ ├── MarkDuplicatesSuite.scala │ │ ├── ReadDatasetSuite.scala │ │ ├── RepairPartitionsSuite.scala │ │ ├── SingleReadBucketSuite.scala │ │ ├── realignment │ │ │ ├── IndelRealignmentTargetSuite.scala │ │ │ ├── ModPartitionerSuite.scala │ │ │ └── RealignIndelsSuite.scala │ │ └── recalibration │ │ │ ├── BaseQualityRecalibrationSuite.scala │ │ │ ├── CycleCovariateSuite.scala │ │ │ ├── DinucCovariateSuite.scala │ │ │ ├── RecalibrationTableSuite.scala │ │ │ └── RecalibratorSuite.scala │ ├── sequence │ │ ├── FlankSlicesSuite.scala │ │ ├── SequenceDatasetSuite.scala │ │ └── SliceDatasetSuite.scala │ └── variant │ │ ├── GenotypeDatasetSuite.scala │ │ ├── VariantContextDatasetSuite.scala │ │ └── VariantDatasetSuite.scala │ ├── io │ ├── InterleavedFastqInputFormatSuite.scala │ └── SingleFastqInputFormatSuite.scala │ ├── models │ ├── AlphabetSuite.scala │ ├── CoverageSuite.scala │ ├── IndelTableSuite.scala │ ├── MdTagSuite.scala │ ├── NonoverlappingRegionsSuite.scala │ ├── ReadGroupDictionarySuite.scala │ ├── ReferencePositionSuite.scala │ ├── ReferenceRegionSuite.scala │ ├── SequenceDictionarySuite.scala │ └── SnpTableSuite.scala │ ├── rich │ ├── RichAlignmentSuite.scala │ └── RichCigarSuite.scala │ └── util │ ├── ADAMFunSuite.scala │ ├── AttributeUtilsSuite.scala │ ├── FileExtensionsSuite.scala │ ├── FileMergerSuite.scala │ ├── IndexedFastaFileSuite.scala │ ├── ParallelFileMergerSuite.scala │ ├── PhredUtilsSuite.scala │ └── TwoBitFileSuite.scala ├── adam-distribution ├── pom.xml └── src │ └── main │ └── assembly │ └── assembly.xml ├── adam-python ├── .gitignore ├── MANIFEST.in ├── Makefile ├── README.md ├── bdgenomics │ ├── __init__.py │ └── adam │ │ ├── .gitignore │ │ ├── __init__.py │ │ ├── adamContext.py │ │ ├── ds.py │ │ ├── find_adam_home.py │ │ ├── models.py │ │ ├── stringency.py │ │ └── test │ │ ├── __init__.py │ │ ├── adamContext_test.py │ │ ├── alignmentDataset_test.py │ │ ├── coverageDataset_test.py │ │ ├── featureDataset_test.py │ │ ├── genotypeDataset_test.py │ │ └── variantDataset_test.py ├── pom.xml ├── setup.py └── version.py ├── adam-r ├── .gitignore ├── bdgenomics.adam │ ├── DESCRIPTION │ ├── NAMESPACE │ ├── R │ │ ├── adam-context.R │ │ ├── ds.R │ │ └── generics.R │ └── tests │ │ ├── testthat.R │ │ └── testthat │ │ ├── helpers.R │ │ ├── test_adamContext.R │ │ ├── test_alignmentDataset.R │ │ ├── test_featureDataset.R │ │ ├── test_genotypeDataset.R │ │ └── test_variantDataset.R └── pom.xml ├── bin ├── adam-shell ├── adam-submit ├── adamR ├── find-adam-assembly.sh ├── find-adam-egg.sh ├── find-adam-home ├── find-spark.sh └── pyadam ├── docs ├── .gitignore ├── Makefile ├── _static │ ├── favicon.ico │ └── logo.png ├── algorithms │ ├── bqsr.rst │ ├── dm.rst │ ├── joins.rst │ ├── reads.rst │ └── ri.rst ├── api │ ├── adamContext.rst │ ├── genomicDataset.rst │ ├── img │ │ ├── join_examples.png │ │ └── join_rdds.png │ ├── joins.rst │ ├── overview.rst │ ├── pipes.rst │ └── python.rst ├── architecture │ ├── evidence.rst │ ├── img │ │ ├── grdd.pdf │ │ ├── grdd.png │ │ ├── stack-model.pdf │ │ └── stack-model.png │ ├── overview.rst │ ├── schemas.rst │ └── stackModel.rst ├── benchmarks │ ├── algorithms.rst │ ├── img │ │ ├── bam.pdf │ │ ├── bam.png │ │ ├── bed.pdf │ │ ├── bed.png │ │ ├── gff.pdf │ │ ├── gff.png │ │ ├── plot-speedup.py │ │ ├── speedup-bqsr.pdf │ │ ├── speedup-bqsr.png │ │ ├── speedup-ir.pdf │ │ ├── speedup-ir.png │ │ ├── speedup-md.pdf │ │ ├── speedup-md.png │ │ ├── vcf.pdf │ │ └── vcf.png │ └── storage.rst ├── citing.rst ├── cli │ ├── actions.rst │ ├── conversions.rst │ ├── overview.rst │ └── printers.rst ├── conf.py ├── deploying │ ├── aws.rst │ ├── gcp.rst │ ├── slurm.rst │ ├── toil.rst │ └── yarn.rst ├── downstream │ ├── cli.rst │ ├── library.rst │ └── overview.rst ├── img │ ├── bdgenomics-stack.key │ ├── bdgenomics-stack.png │ ├── source │ │ └── file_benchmarks.py │ └── stack-model.ai ├── index.rst ├── installation │ ├── example.rst │ ├── pip.rst │ └── source.rst ├── references.rst ├── requirements.txt ├── source │ └── bibliography.bib └── template.tex ├── pom.xml └── scripts ├── fastq-interleaver.py ├── make-flag-values-sam.py ├── move_to_scala_2.11.sh ├── move_to_scala_2.12.sh ├── move_to_spark_2.sh ├── move_to_spark_3.sh └── release.sh 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