LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
pymisha/__init__.py
pymisha/_array_track.py
pymisha/_crc64.py
pymisha/_db_trash.py
pymisha/_iterator_policy.py
pymisha/_name_validation.py
pymisha/_pymisha.pyi
pymisha/_quadtree.py
pymisha/_r_serialize.py
pymisha/_safe_eval.py
pymisha/_safe_pickle.py
pymisha/_shared.py
pymisha/_types.py
pymisha/analysis.py
pymisha/dataset.py
pymisha/db.py
pymisha/db_attrs.py
pymisha/db_create.py
pymisha/expr.py
pymisha/extract.py
pymisha/gdir.py
pymisha/genome_edit.py
pymisha/gsynth.py
pymisha/intervals.py
pymisha/intervals_attr.py
pymisha/intervals_mat.py
pymisha/liftover.py
pymisha/lookup.py
pymisha/motif_import.py
pymisha/py.typed
pymisha/sequence.py
pymisha/summary.py
pymisha/track_export.py
pymisha/tracks.py
pymisha/vtracks.py
pymisha.egg-info/PKG-INFO
pymisha.egg-info/SOURCES.txt
pymisha.egg-info/dependency_links.txt
pymisha.egg-info/not-zip-safe
pymisha.egg-info/requires.txt
pymisha.egg-info/top_level.txt
pymisha/examples/trackdb/test/.db.cache
pymisha/examples/trackdb/test/.ro_attributes
pymisha/examples/trackdb/test/chrom_sizes.txt
pymisha/examples/trackdb/test/reads
pymisha/examples/trackdb/test/data/test.chain
pymisha/examples/trackdb/test/pssms/pssm.data
pymisha/examples/trackdb/test/pssms/pssm.key
pymisha/examples/trackdb/test/seq/chr1.seq
pymisha/examples/trackdb/test/seq/chr2.seq
pymisha/examples/trackdb/test/seq/chrX.seq
pymisha/examples/trackdb/test/tracks/annotations.interv
pymisha/examples/trackdb/test/tracks/array_track.track/.attributes
pymisha/examples/trackdb/test/tracks/array_track.track/.attributes.yaml
pymisha/examples/trackdb/test/tracks/array_track.track/.colnames
pymisha/examples/trackdb/test/tracks/array_track.track/chr1
pymisha/examples/trackdb/test/tracks/array_track.track/chr2
pymisha/examples/trackdb/test/tracks/array_track.track/chrX
pymisha/examples/trackdb/test/tracks/dense_track.track/.attributes
pymisha/examples/trackdb/test/tracks/dense_track.track/.attributes.yaml
pymisha/examples/trackdb/test/tracks/dense_track.track/chr1
pymisha/examples/trackdb/test/tracks/dense_track.track/chr2
pymisha/examples/trackdb/test/tracks/dense_track.track/chrX
pymisha/examples/trackdb/test/tracks/dense_track.track/vars/pv.percentiles
pymisha/examples/trackdb/test/tracks/rects_track.track/.attributes
pymisha/examples/trackdb/test/tracks/rects_track.track/.attributes.yaml
pymisha/examples/trackdb/test/tracks/rects_track.track/chr1-chr1
pymisha/examples/trackdb/test/tracks/rects_track.track/chr1-chr2
pymisha/examples/trackdb/test/tracks/rects_track.track/chr1-chrX
pymisha/examples/trackdb/test/tracks/sparse_track.track/.attributes
pymisha/examples/trackdb/test/tracks/sparse_track.track/.attributes.yaml
pymisha/examples/trackdb/test/tracks/sparse_track.track/chr1
pymisha/examples/trackdb/test/tracks/sparse_track.track/chr2
pymisha/examples/trackdb/test/tracks/sparse_track.track/chrX
pymisha/examples/trackdb/test/tracks/subdir/dense_track2.track/.attributes
pymisha/examples/trackdb/test/tracks/subdir/dense_track2.track/.attributes.yaml
pymisha/examples/trackdb/test/tracks/subdir/dense_track2.track/chr1
pymisha/examples/trackdb/test/tracks/subdir/dense_track2.track/chr2
pymisha/examples/trackdb/test/tracks/subdir/dense_track2.track/chrX
pymisha/genome/__init__.py
pymisha/genome/_build_seq.py
pymisha/genome/_chrom_alias.py
pymisha/genome/_gtf.py
pymisha/genome/_http.py
pymisha/genome/_hub.py
pymisha/genome/_install_sets.py
pymisha/genome/_ncbi.py
pymisha/genome/_ucsc.py
pymisha/genome/recipes.yaml
pymisha/genome/registry.py
src/BinFinder.cpp
src/BinFinder.h
src/BinsManager.h
src/BufferedFile.cpp
src/BufferedFile.h
src/CRC64.h
src/DnaPSSM.cpp
src/DnaPSSM.h
src/GInterval.cpp
src/GInterval.h
src/GInterval2D.h
src/GenomeChromKey.h
src/GenomeIndex.cpp
src/GenomeIndex.h
src/GenomeSeqFetch.cpp
src/GenomeSeqFetch.h
src/GenomeSeqScorer.cpp
src/GenomeSeqScorer.h
src/GenomeTrack.cpp
src/GenomeTrack.h
src/GenomeTrack1D.h
src/GenomeTrackArray.cpp
src/GenomeTrackArray.h
src/GenomeTrackFixedBin.cpp
src/GenomeTrackFixedBin.h
src/GenomeTrackSparse.cpp
src/GenomeTrackSparse.h
src/GenomeUtils.cpp
src/GenomeUtils.h
src/HashFunc.h
src/IncrementalWilcox.cpp
src/IncrementalWilcox.h
src/IndexedTrackWriter.cpp
src/IndexedTrackWriter.h
src/KmerCounter.cpp
src/KmerCounter.h
src/MaskUtils.h
src/MaskedBpCounter.cpp
src/MaskedBpCounter.h
src/MemQuadTree.cpp
src/MemQuadTree.h
src/MmapFile.h
src/PMChainIntervals.cpp
src/PMChainIntervals.h
src/PMChainParser.cpp
src/PMComputeStrandsAutocorr.cpp
src/PMCrc64.cpp
src/PMDataFrame.cpp
src/PMDataFrame.h
src/PMDb.cpp
src/PMDb.h
src/PMDirectAccumulator.h
src/PMFindNeighbors.cpp
src/PMGTrackLiftover.cpp
src/PMGTrackLiftover2D.cpp
src/PMGenomeEditImplant.cpp
src/PMGenomeTrack2D.cpp
src/PMGenomeTrack2D.h
src/PMGseqPwmEdits.cpp
src/PMGsynth.cpp
src/PMImportMappedseq.cpp
src/PMImportMappedseq.h
src/PMIntervalsRandom.cpp
src/PMKmerCountStrings.cpp
src/PMLiftoverAggregate.cpp
src/PMLiftoverAggregate.h
src/PMObject.h
src/PMPwmScoreStrings.cpp
src/PMSourceTrack.cpp
src/PMSourceTrack.h
src/PMSourceTrack2D.cpp
src/PMSourceTrack2D.h
src/PMStubs.cpp
src/PMTrack2DIndexedFormat.cpp
src/PMTrackCreate.cpp
src/PMTrackExpression2DIterator.cpp
src/PMTrackExpression2DIterator.h
src/PMTrackExpression2DIteratorPolicy.cpp
src/PMTrackExpression2DIteratorPolicy.h
src/PMTrackExpression2DScanner.cpp
src/PMTrackExpression2DScanner.h
src/PMTrackExpression2DVars.cpp
src/PMTrackExpression2DVars.h
src/PMTrackExpressionCartesianGridIterator.cpp
src/PMTrackExpressionCartesianGridIterator.h
src/PMTrackExpressionFixedRectIterator.cpp
src/PMTrackExpressionFixedRectIterator.h
src/PMTrackExpressionIterator.cpp
src/PMTrackExpressionIterator.h
src/PMTrackExpressionScanner.cpp
src/PMTrackExpressionScanner.h
src/PMTrackExpressionTrackRectsIterator.cpp
src/PMTrackExpressionTrackRectsIterator.h
src/PMTrackExpressionVars.cpp
src/PMTrackExpressionVars.h
src/PMTrackIndexedFormat.cpp
src/PMTrackSplitIndexed.cpp
src/PMVTrack.cpp
src/PMWigImport.cpp
src/PMWilcox.cpp
src/PWMEditDistanceScorer.cpp
src/PWMEditDistanceScorer.h
src/PWMLseEditDistanceScorer.cpp
src/PWMLseEditDistanceScorer.h
src/PWMScorer.cpp
src/PWMScorer.h
src/QuadTreeReader.cpp
src/QuadTreeReader.h
src/RaList.h
src/Random.h
src/RandomShuffle.h
src/Segment.h
src/SegmentFinder.h
src/StratifiedMarkovModel.cpp
src/StratifiedMarkovModel.h
src/StreamPercentiler.h
src/StreamSampler.h
src/TGLException.cpp
src/TGLException.h
src/TrackIndex.cpp
src/TrackIndex.h
src/TrackIndex2D.cpp
src/TrackIndex2D.h
src/config.h
src/pmutils.h
src/port.h
src/pymisha.cpp
src/pymisha.h
src/pymisha_init.cpp
src/util.h
src/utils/RunningLogSumExp.h
src/utils/RunningMaxDeque.h
tests/test_2d_band_coord_clipping.py
tests/test_2d_band_cpp.py
tests/test_2d_import_multifile.py
tests/test_2d_iterator.py
tests/test_2d_multi_track_compound.py
tests/test_2d_scanner_chrom_prefix.py
tests/test_2d_scanner_iterator.py
tests/test_2d_scanner_vars.py
tests/test_2d_set_ops.py
tests/test_2d_vtrack_nonag.py
tests/test_2d_vtrack_shifts_scanner.py
tests/test_2d_vtracks_aggregation.py
tests/test_annotate_tie.py
tests/test_api_type_gaps.py
tests/test_array_track_scanner.py
tests/test_band_intersect.py
tests/test_benchmarks.py
tests/test_chain_intervals_resolve_cpp.py
tests/test_chain_parser_cpp.py
tests/test_chrom_alias_min_coverage.py
tests/test_cis_decay_perf.py
tests/test_computed_tracks.py
tests/test_cpp_coverage_gaps.py
tests/test_create_dense_func.py
tests/test_dataset_and_alias.py
tests/test_dataset_resolution.py
tests/test_db_admin.py
tests/test_db_trash.py
tests/test_dbs_functions.py
tests/test_dim_param.py
tests/test_expr_aliasing.py
tests/test_expr_logical_precedence.py
tests/test_expr_user_vars.py
tests/test_extract_2d_fast.py
tests/test_extract_2d_objects_fast.py
tests/test_fd_safety.py
tests/test_force_range_extra_cols.py
tests/test_gbins.py
tests/test_gcis_decay.py
tests/test_gcor.py
tests/test_gdataset_example.py
tests/test_gdb_cache_dirty.py
tests/test_gdb_convert_to_indexed.py
tests/test_gdb_create.py
tests/test_gdb_export_fasta.py
tests/test_gdb_info.py
tests/test_gdir.py
tests/test_gdist.py
tests/test_gdist_vtrack_streaming.py
tests/test_genome_build_genome_skel.py
tests/test_genome_build_manual.py
tests/test_genome_chrom_alias.py
tests/test_genome_chrom_alias_rescue.py
tests/test_genome_gtf.py
tests/test_genome_http.py
tests/test_genome_hub_assets.py
tests/test_genome_install_genes.py
tests/test_genome_install_intervals.py
tests/test_genome_install_rmsk_cgi_cytoband.py
tests/test_genome_ncbi.py
tests/test_genome_ncbi_fetch.py
tests/test_genome_network.py
tests/test_genome_registry.py
tests/test_genome_ucsc_assets.py
tests/test_gextract.py
tests/test_gextract_2d.py
tests/test_gextract_2d_df_iterator.py
tests/test_gextract_colnames.py
tests/test_gextract_intervals_join.py
tests/test_gextract_output.py
tests/test_ggenome.py
tests/test_gintervals.py
tests/test_gintervals_attr.py
tests/test_gintervals_constructors.py
tests/test_gintervals_import_genes.py
tests/test_gintervals_load_save.py
tests/test_gintervals_management.py
tests/test_gintervals_mapply.py
tests/test_gintervals_neighbors.py
tests/test_gintervals_neighbors_directional.py
tests/test_gintervals_random_cpp.py
tests/test_gintervals_summary_quantiles.py
tests/test_gintervals_to_mat.py
tests/test_gintervals_update.py
tests/test_gintervals_utils.py
tests/test_giterator_cartesian_grid.py
tests/test_glookup.py
tests/test_glookup_streaming.py
tests/test_golden_master.py
tests/test_golden_master_advanced_intervals.py
tests/test_golden_master_iterator.py
tests/test_golden_master_liftover.py
tests/test_golden_master_sequence.py
tests/test_golden_master_stats.py
tests/test_golden_master_vtracks.py
tests/test_gpartition.py
tests/test_gquantiles.py
tests/test_grevcomp.py
tests/test_gsample.py
tests/test_gsegment.py
tests/test_gseq.py
tests/test_gseq_kmer.py
tests/test_gseq_pwm.py
tests/test_gseq_pwm_cpp.py
tests/test_gseq_pwm_spatial.py
tests/test_gsummary.py
tests/test_gsynth.py
tests/test_gsynth_0d_unaligned.py
tests/test_gsynth_cell_merge.py
tests/test_gsynth_fai.py
tests/test_gsynth_forbid.py
tests/test_gsynth_parallel.py
tests/test_gtrack_2d_nan_retention.py
tests/test_gtrack_array.py
tests/test_gtrack_atomic.py
tests/test_gtrack_attr.py
tests/test_gtrack_attr_import.py
tests/test_gtrack_copy_crossdb.py
tests/test_gtrack_create_empty_indexed.py
tests/test_gtrack_create_pwm_energy.py
tests/test_gtrack_exists.py
tests/test_gtrack_liftover_2d_cpp.py
tests/test_gtrack_liftover_cpp.py
tests/test_gtrack_lookup.py
tests/test_gtrack_ls.py
tests/test_gtrack_var.py
tests/test_gvtrack_filter.py
tests/test_gwilcox.py
tests/test_import_contacts.py
tests/test_import_mappedseq_bam.py
tests/test_import_mappedseq_cpp.py
tests/test_indexed_cache_invalidation.py
tests/test_indexed_empty_leading_chrom.py
tests/test_init_exports.py
tests/test_install_genes_names.py
tests/test_intersect_2d_scalable.py
tests/test_intervals_2d.py
tests/test_intervals_indexed.py
tests/test_intervals_iterator.py
tests/test_intervals_set_out.py
tests/test_intra_chrom_parallel.py
tests/test_iterator_cartesian_grid.py
tests/test_iterator_fixed_rect.py
tests/test_iterator_intervals_via_scanner.py
tests/test_iterator_policy.py
tests/test_iterator_track_name.py
tests/test_iterator_track_rects.py
tests/test_liftover.py
tests/test_liftover_aggregate_cpp.py
tests/test_map_intervals_cpp.py
tests/test_motif_import.py
tests/test_multi_db.py
tests/test_multiprocess.py
tests/test_multiprocess_review.py
tests/test_multitask.py
tests/test_multitask_strategy.py
tests/test_named_intervals.py
tests/test_ncbi_install_genes_fallback.py
tests/test_neighbors_2d.py
tests/test_neighbors_2d_nn.py
tests/test_optimization_summary.py
tests/test_path_functions.py
tests/test_pm_test_cartesian_grid_iterator.py
tests/test_pm_test_fixed_rect_iterator.py
tests/test_pm_test_track_rects_iterator.py
tests/test_pwm_edit_distance.py
tests/test_pwm_score_strings_smoke.py
tests/test_pwm_sliding_window.py
tests/test_pwm_spatial.py
tests/test_quadtree_cpp.py
tests/test_quadtree_query.py
tests/test_r_serialize.py
tests/test_security_robustness.py
tests/test_source_track_2d_cpp.py
tests/test_source_track_cpp.py
tests/test_sparse_stddev_constant.py
tests/test_strands_autocorr.py
tests/test_track2d.py
tests/test_track2d_indexed.py
tests/test_track_create_direct_indexed.py
tests/test_track_create_import.py
tests/test_track_export.py
tests/test_track_indexed.py
tests/test_track_liftover.py
tests/test_track_liftover_fixed_bin.py
tests/test_track_modify_smooth.py
tests/test_trans_mirroring.py
tests/test_vtrack_cpp_path.py
tests/test_vtrack_distance_center.py
tests/test_vtrack_distance_center_overlap.py
tests/test_vtrack_distance_nearest_trap.py
tests/test_vtrack_iterator_2d.py
tests/test_vtrack_lse.py
tests/test_vtracks.py
tests/test_wig_cpp.py