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