├── .gitignore ├── .gitmodules ├── README.md ├── dist └── svtk-0.1-py3.5-linux-x86_64.egg ├── scripts └── svtk ├── setup.py └── svtk ├── __init__.py ├── adjudicate ├── __init__.py ├── adjudicate_sv.py ├── labelers.py └── random_forest.py ├── annotation ├── __init__.py ├── annotate.py ├── annotate_intersection.py ├── classify_effect.py └── nearest_tss.py ├── baf └── BAFpysam.py ├── cli ├── __init__.py ├── adjudicate.py ├── annotate.py ├── baf_test.py ├── bedcluster.py ├── bincov.py ├── collect_pesr.py ├── count_svtypes.py ├── pesr_test.py ├── rdtest2vcf.py ├── resolve.py ├── standardize_vcf.py ├── utils.py └── vcfcluster.py ├── cxsv ├── __init__.py ├── complex_sv.py ├── cpx_inv.py ├── cpx_link.py ├── cpx_tloc.py └── rescan_single_enders.py ├── data ├── GRCh37_template.vcf ├── no_contigs_template.vcf └── vcfcluster_template.vcf ├── famfile.py ├── genomeslink.py ├── pesr ├── __init__.py ├── breakpoint.py ├── pe_test.py ├── pesr_test.py └── sr_test.py ├── standardize ├── __init__.py ├── 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