LICENSE.txt
README.md
pyproject.toml
handygenome/align/__init__.py
handygenome/align/alignhandler.py
handygenome/align/msa.py
handygenome/align/pairwise.py
handygenome/align/realign_legacy_pysampileup_mypileup_comparison.py
handygenome/align/realign_using_fetchedreads.py
handygenome/align/toolwrapper.py
handygenome/align/realign/base.py
handygenome/align/realign/msrpileup.py
handygenome/align/realign/msrpileup_series.py
handygenome/align/realign/rpileup.py
handygenome/align/realign/rpileup_series.py
handygenome/analysis/__init__.py
handygenome/analysis/driver.py
handygenome/analysis/feature.py
handygenome/annotation/__init__.py
handygenome/annotation/annotitem.py
handygenome/annotation/annotitem_deprecated.py
handygenome/annotation/callerinfo.py
handygenome/annotation/cosmic.py
handygenome/annotation/customfile.py
handygenome/annotation/customfile_deprecated.py
handygenome/annotation/data.py
handygenome/annotation/ensembl_feature.py
handygenome/annotation/ensembl_parser.py
handygenome/annotation/ensembl_parser_deprecated.py
handygenome/annotation/ensembl_rest.py
handygenome/annotation/feature.py
handygenome/annotation/genotype.py
handygenome/annotation/oncokb.py
handygenome/annotation/popfreq.py
handygenome/annotation/readstats.py
handygenome/annotation/rnalib.py
handygenome/annotation/veplib.py
handygenome/bin/__init__.py
handygenome/bin/alleleindex_annotator.py
handygenome/bin/annotate_all.py
handygenome/bin/bismark_to_vcf.py
handygenome/bin/caller_postprocessor.py
handygenome/bin/concat_vcf.py
handygenome/bin/merge_vcf.py
handygenome/bin/readstats_annotator.py
handygenome/bin/split_vcf.py
handygenome/bin/strelka_postprocessor.py
handygenome/bin/strip_vcf.py
handygenome/bin/varscan_postprocessor.py
handygenome/bin/database_converter/__init__.py
handygenome/bin/database_converter/cosmic_converter.py
handygenome/bin/database_converter/dbsnp_converter.py
handygenome/bin/database_converter/geneset_converter.py
handygenome/bin/database_converter/regulatory_converter.py
handygenome/bin/database_converter/repeat_converter.py
handygenome/bin/slurmutils/__init__.py
handygenome/bin/slurmutils/sbatch_helper.py
handygenome/bin/tool_wrappers/HaplotypeCaller_wrapper.py
handygenome/bin/tool_wrappers/VarScan2_wrapper.py
handygenome/bin/tool_wrappers/seqz_maker.py
handygenome/cnv/__init__.py
handygenome/cnv/baf.py
handygenome/cnv/cnvbrowser.py
handygenome/cnv/gcfraction.py
handygenome/cnv/gcfraction_old.py
handygenome/cnv/make_seqz.py
handygenome/cnv/misc.py
handygenome/cnv/misc_oldver_230222.py
handygenome/cnv/mosdepth.py
handygenome/cnv/rcopynumber.py
handygenome/cnv/read_cnvfile.py
handygenome/cnv/sequenza_handler.py
handygenome/cnv/sequenza_utils.py
handygenome/dbconv/__init__.py
handygenome/dbconv/cosmicdb.py
handygenome/dbconv/dbsnp.py
handygenome/handygenome.egg-info/PKG-INFO
handygenome/handygenome.egg-info/SOURCES.txt
handygenome/handygenome.egg-info/dependency_links.txt
handygenome/handygenome.egg-info/requires.txt
handygenome/handygenome.egg-info/top_level.txt
handygenome/plot/__init__.py
handygenome/plot/circos.py
handygenome/plot/filterinfo.py
handygenome/plot/genomeplot.py
handygenome/plot/heatmap.py
handygenome/plot/misc.py
handygenome/publicdb/__init__.py
handygenome/publicdb/ensembl_download.py
handygenome/publicdb/ncbi.py
handygenome/publicdb/ncbi_postprocess.py
handygenome/read/__init__.py
handygenome/read/alleleinfo.py
handygenome/read/alleleinfo_sv.py
handygenome/read/fetchcache.py
handygenome/read/pileup.py
handygenome/read/pileup_using_fetchedreads.py
handygenome/read/readhandler.py
handygenome/read/readplus.py
handygenome/ria_deprecated/__init__.py
handygenome/ria_deprecated/edit_readplus.py
handygenome/ria_deprecated/edit_readpluspair.py
handygenome/ria_deprecated/get_alleleclass_from_readplus.py
handygenome/ria_deprecated/get_alleleclass_from_readpluspair.py
handygenome/ria_deprecated/main.py
handygenome/signature/cataloguing.py
handygenome/signature/misc.py
handygenome/signature/plotter_sbs96.py
handygenome/signature/signatureresult.py
handygenome/signature/sigprofiler.py
handygenome/sigprofiler_clone/__init__.py
handygenome/sigprofiler_clone/SigProfilerAssignment/Analyzer.py
handygenome/sigprofiler_clone/SigProfilerAssignment/__init__.py
handygenome/sigprofiler_clone/SigProfilerAssignment/decompose_subroutines.py
handygenome/sigprofiler_clone/SigProfilerAssignment/decomposition.py
handygenome/sigprofiler_clone/SigProfilerAssignment/single_sample.py
handygenome/sigprofiler_clone/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py
handygenome/sigprofiler_clone/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py
handygenome/sigprofiler_clone/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py
handygenome/sigprofiler_clone/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_ID83.py
handygenome/sigprofiler_clone/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS1536.py
handygenome/sigprofiler_clone/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS288.py
handygenome/sigprofiler_clone/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS96.py
handygenome/sigprofiler_clone/SigProfilerAssignment/DecompositionPlots/SigProfilerPlottingMatrix.py
handygenome/sigprofiler_clone/SigProfilerExtractor/__init__.py
handygenome/sigprofiler_clone/SigProfilerExtractor/estimate_best_solution.py
handygenome/sigprofiler_clone/SigProfilerExtractor/nmf_cpu.py
handygenome/sigprofiler_clone/SigProfilerExtractor/nmf_gpu.py
handygenome/sigprofiler_clone/SigProfilerExtractor/sigpro.py
handygenome/sigprofiler_clone/SigProfilerExtractor/subroutines.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/install.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/chromosomes/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/chromosomes/exome/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/chromosomes/transcripts/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/chromosomes/tsb/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/chromosomes/tsb_BED/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/matrix/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/vcf_files/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/vcf_files/BED/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/vcf_files/BRCA_example/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/vcf_files/BRCA_example/SNV/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/references/vcf_files/GRCh37_bench/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/CNVMatrixGenerator.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/SVMatrixGenerator.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGenerator.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/__init__.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/convert_input_to_simple_files.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/save_chrom_strings.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/save_chrom_tsb_separate.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/save_context_distribution.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/save_tsb_192.py
handygenome/sigprofiler_clone/SigProfilerMatrixGenerator/scripts/Benchmark/__init__.py
handygenome/sv/__init__.py
handygenome/sv/breakends.py
handygenome/sv/structvars.py
handygenome/sv/svcall.py
handygenome/sv/svreader.py
handygenome/svtools_deprecated/__init__.py
handygenome/svtools_deprecated/concat.py
handygenome/svtools_deprecated/variant_plus_modifiers.py
handygenome/variant/__init__.py
handygenome/variant/alleleindexes.py
handygenome/variant/filter.py
handygenome/variant/infoformat.py
handygenome/variant/ponbams.py
handygenome/variant/repeat.py
handygenome/variant/svcaller_parser.py
handygenome/variant/varianthandler.py
handygenome/variant/variantplus.py
handygenome/variant/vcfspec.py
handygenome/variant/deprecated/variantplus.py
handygenome/vcfeditor/__init__.py
handygenome/vcfeditor/concat.py
handygenome/vcfeditor/headerhandler.py
handygenome/vcfeditor/indexing.py
handygenome/vcfeditor/initvcf.py
handygenome/vcfeditor/merge.py
handygenome/vcfeditor/misc.py
handygenome/vcfeditor/split.py
handygenome/vcfeditor/varscan_editing.py
handygenome/workflow/__init__.py
handygenome/workflow/toolsetup.py