├── .gitignore ├── GENOTYPE.md ├── LICENSE ├── README.md ├── Snakefile ├── bin └── trf ├── cluster.eichler.json ├── cluster.template.json ├── dep ├── .gitignore ├── Makefile ├── conda │ ├── .gitignore │ ├── Makefile │ ├── install_pacbio.sh │ ├── install_python2.sh │ ├── install_python3.sh │ └── install_tools.sh ├── python_dummy │ └── python_dummy.sh └── smrtsvtools │ ├── .gitignore │ ├── Makefile │ ├── include │ ├── phase │ │ ├── PhaseTable.h │ │ ├── PhaseWriter.h │ │ ├── ReadPhaser.h │ │ ├── SNVEntry.h │ │ └── StringUtil.h │ └── util │ │ ├── constants.h │ │ └── err.h │ └── src │ ├── alignfixup.cpp │ ├── hdrtest.cpp │ ├── phase │ ├── PhaseTable.cpp │ ├── PhaseWriter.cpp │ ├── ReadPhaser.cpp │ ├── SNVEntry.cpp │ └── StringUtil.cpp │ ├── phasereads.cpp │ ├── tlenadd.cpp │ └── util │ └── err.cpp ├── files ├── call │ └── rmsk_empty ├── examples │ └── gt │ │ ├── genotyper.json │ │ └── samples.tab └── gtmodel │ ├── 30x-4 │ ├── cv │ │ ├── samples │ │ │ ├── PSEUDO_10x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_15x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_20x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_30x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_40x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_4x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_50x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_5x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_60x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_6x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ ├── PSEUDO_7x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ │ └── PSEUDO_8x │ │ │ │ ├── model_predict.tab.gz │ │ │ │ ├── predict_prop.tab.gz │ │ │ │ └── stats.tab.gz │ │ ├── stats.tab.gz │ │ ├── test_sets.tab.gz │ │ └── test_sets_nosel.tab.gz │ ├── gt_learn.json │ └── model │ │ ├── X.npy │ │ ├── features.tab.gz │ │ ├── features_summary.tab.gz │ │ ├── predictor.pkl │ │ ├── predictor_stats.tab.gz │ │ ├── scaler.pkl │ │ └── y.npy │ └── 8x-2 │ ├── cv │ ├── samples │ │ ├── PSEUDO_10x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_15x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_20x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_30x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_40x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_4x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_50x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_5x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_60x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_6x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ ├── PSEUDO_7x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ │ └── PSEUDO_8x │ │ │ ├── model_predict.tab.gz │ │ │ ├── predict_prop.tab.gz │ │ │ └── stats.tab.gz │ ├── stats.tab.gz │ ├── test_sets.tab.gz │ └── test_sets_nosel.tab.gz │ ├── gt_learn.json │ └── model │ ├── X.npy │ ├── features.tab.gz │ ├── features_summary.tab.gz │ ├── predictor.pkl │ ├── predictor_stats.tab.gz │ ├── scaler.pkl │ └── y.npy ├── rules ├── align.snakefile ├── assemble.snakefile ├── assemble_group.snakefile ├── call.snakefile ├── detect.snakefile ├── genotype.snakefile ├── genotype_learn.snakefile ├── genotype_map.snakefile ├── include.snakefile ├── plots │ ├── detect.snakefile │ └── genotype.snakefile └── reference.snakefile ├── runsnake.py ├── scripts ├── PrintGaps.py ├── assemble │ └── BamToFasta.py ├── call │ ├── AnnotateGapBed.py │ ├── AnnotateWithTRF.py │ ├── BedIntervalsToDepth.py │ ├── BedMod.py │ ├── FilterGapsByTilingPath.py │ ├── FixMasked.py │ ├── GapBedToFasta.py │ ├── PrintSNVSupport.py │ ├── PrintUniqueEvents.py │ ├── TilingPath.py │ ├── cluster_calls.py │ └── variants_bed_to_vcf.py ├── detect │ ├── PrintGapSupport.py │ ├── find_fasta_gaps.py │ └── plot_SV_candidate_summary.R ├── genotype │ ├── FilterContigs.py │ ├── FilterFastqHardmask.py │ ├── FragmentFastaRecords.py │ ├── GetBreakpointReadDepth.py │ ├── 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