├── .github └── workflows │ ├── build-test-pyd4.yml │ └── push-check.yml ├── .gitignore ├── .vscode ├── c_cpp_properties.json ├── launch.json └── settings.json ├── Cargo.toml ├── Dockerfile ├── LICENSE ├── README.md ├── d4-bigwig ├── Cargo.toml ├── bigwig_inc.h ├── build-lib.sh ├── build.rs ├── generated │ └── bigwig.rs └── src │ ├── bigwig_sys.rs │ └── lib.rs ├── d4-framefile ├── Cargo.toml └── src │ ├── blob.rs │ ├── directory.rs │ ├── lib.rs │ ├── mapped.rs │ ├── randfile.rs │ └── stream.rs ├── d4-hts ├── Cargo.toml ├── LICENSE ├── build.rs ├── build_htslib.sh ├── generated │ └── hts.rs ├── hts_inc.h └── src │ ├── alignment │ ├── alignment_ext.rs │ ├── alignment_impl.rs │ ├── bamfile.rs │ ├── cigar_ext.rs │ ├── error.rs │ ├── htslib.rs │ ├── map_ext.rs │ ├── mod.rs │ ├── nucleotide.rs │ └── seq_ext.rs │ └── lib.rs ├── d4 ├── Cargo.toml ├── examples │ ├── count_min_depth_pos_mt.rs │ └── find_de_novo.rs └── src │ ├── chrom.rs │ ├── d4file │ ├── merger.rs │ ├── mod.rs │ ├── reader.rs │ ├── track.rs │ └── writer.rs │ ├── dict.rs │ ├── header.rs │ ├── index │ ├── data_index │ │ ├── data.rs │ │ └── mod.rs │ ├── mod.rs │ └── sfi.rs │ ├── lib.rs │ ├── ptab │ ├── bit_array.rs │ └── mod.rs │ ├── ssio │ ├── http.rs │ ├── mod.rs │ ├── reader.rs │ ├── table.rs │ └── view.rs │ ├── stab │ ├── mod.rs │ └── sparse_array │ │ ├── compression.rs │ │ ├── mod.rs │ │ ├── reader.rs │ │ ├── record.rs │ │ ├── record_block.rs │ │ └── writer.rs │ └── task │ ├── context.rs │ ├── histogram.rs │ ├── mean.rs │ ├── mod.rs │ ├── perc_cov.rs │ ├── sum.rs │ ├── value_range.rs │ └── vector.rs ├── d4binding ├── Cargo.toml ├── README.md ├── bindgen │ └── c_api.rs ├── build.rs ├── d4binding.pc.in ├── example │ ├── Makefile │ ├── create.c │ ├── error.c │ ├── mean-depth.c │ ├── multithread-read.c │ ├── read-index.c │ ├── read-interval.c │ └── read.c ├── include │ └── d4.h ├── install.sh └── src │ ├── api.rs │ ├── c_api.rs │ ├── handle.rs │ ├── lib.rs │ ├── stream.rs │ └── task.rs ├── d4tools ├── Cargo.toml ├── src │ ├── create │ │ ├── cli.yml │ │ ├── main.rs │ │ └── mod.rs │ ├── framedump │ │ ├── main.rs │ │ └── mod.rs │ ├── index │ │ ├── cli.yml │ │ ├── main.rs │ │ └── mod.rs │ ├── lib.rs │ ├── ls_track │ │ ├── cli.yml │ │ ├── main.rs │ │ └── mod.rs │ ├── main.rs │ ├── merge │ │ ├── cli.yml │ │ ├── main.rs │ │ └── mod.rs │ ├── plot │ │ ├── cli.yml │ │ └── mod.rs │ ├── server │ │ ├── cli.yml │ │ ├── main.rs │ │ └── mod.rs │ ├── show │ │ ├── cli.yml │ │ ├── main.rs │ │ └── mod.rs │ └── stat │ │ ├── cli.yml │ │ ├── main.rs │ │ └── mod.rs └── test │ ├── .gitignore │ ├── create │ ├── fractional-bedgraph-fixed-denominator │ │ ├── cmdline │ │ ├── genome.size │ │ ├── input.bedgraph │ │ └── output.txt │ ├── fractional-bedgraph │ │ ├── cmdline │ │ ├── genome.size │ │ ├── input.bedgraph │ │ └── output.txt │ ├── from-bam │ │ ├── cmdline │ │ ├── output.txt │ │ ├── small.bam │ │ └── small.bam.bai │ ├── from-bedgraph │ │ ├── cmdline │ │ ├── genome.size │ │ ├── input.bedgraph │ │ └── output.txt │ ├── from-bigwig │ │ ├── cmdline │ │ ├── input.bw │ │ └── output.txt │ ├── multiple-sequences-check │ │ ├── cmdline │ │ ├── multi_reads_multi_chr.bam │ │ ├── multi_reads_multi_chr.bam.bai │ │ └── output.txt │ └── single-read │ │ ├── cmdline │ │ ├── output.txt │ │ ├── single_read.bai │ │ └── single_read.bam │ ├── data │ ├── cross_chunk_regions.bed │ ├── hg002_full_no_cov.d4 │ ├── index-test.bedgraph │ ├── index-test.genomesize │ ├── input.d4 │ ├── input_10nt.d4 │ ├── input_10nt.multiple_ranges.bed │ ├── input_10nt.overlapping_ranges.bed │ └── multitrack.d4 │ ├── index │ └── build │ │ ├── cmdline │ │ └── output.txt │ ├── regression │ └── issue52 │ │ ├── cmdline │ │ ├── input.d4 │ │ └── output.txt │ ├── show │ ├── basic-view │ │ ├── cmdline │ │ └── output.txt │ ├── remote-view-multitrack │ │ ├── cmdline │ │ └── output.txt │ ├── remote-view │ │ ├── cmdline │ │ └── output.txt │ ├── view-multitrack │ │ ├── cmdline │ │ └── output.txt │ ├── view-one-track │ │ ├── cmdline │ │ └── output.txt │ ├── view-region │ │ ├── cmdline │ │ └── output.txt │ └── view-with-header │ │ ├── cmdline │ │ └── output.txt │ ├── stat │ ├── cross-chunk-boundary-stat │ │ ├── cmdline │ │ └── output.txt │ ├── mean-multiple-ranges │ │ ├── cmdline │ │ └── output.txt │ ├── mean-overlapping-range │ │ ├── cmdline │ │ └── output.txt │ ├── mean │ │ ├── cmdline │ │ └── output.txt │ ├── median │ │ ├── cmdline │ │ └── output.txt │ ├── multitrack-mean │ │ ├── cmdline │ │ └── output.txt │ ├── perc_cov-multiple-ranges │ │ ├── cmdline │ │ └── output.txt │ ├── perc_cov-overlapping-range │ │ ├── cmdline │ │ └── output.txt │ └── region-stat │ │ ├── cmdline │ │ ├── output.txt │ │ └── windows.bed │ └── test-driver ├── example.sh ├── latest_version ├── publish.sh ├── pyd4 ├── .gitignore ├── Cargo.toml ├── MANIFEST.in ├── README.md ├── examples │ ├── .gitignore │ ├── D4 Tutorial in Python.ipynb │ ├── d4toh5.py │ ├── dump-np-as-d4.py │ ├── load-to-np.py │ ├── multi-track-values.py │ ├── values.py │ └── window.py ├── pyproject.toml ├── python │ └── pyd4 │ │ └── __init__.py ├── src │ ├── builder.rs │ ├── d4file.rs │ ├── iter.rs │ └── lib.rs └── tests │ ├── __init__.py │ └── test_pyd4.py └── scripts-for-manuscript ├── figure1_3 ├── Cargo.toml └── src │ └── main.rs ├── figure4 ├── config.sh ├── creation-scalability.sh ├── make-hdf5.sh ├── process-result.sh ├── rand-acc-scalability.sh ├── run-all.sh ├── seq-acc-scalability.sh ├── src │ ├── bgzf-mean-random.sh │ ├── bgzf-mean │ │ ├── build.sh │ │ └── mean.c │ ├── bw-mean-random │ │ ├── build.sh │ │ └── bw-mean.c │ ├── bw-mean │ │ ├── build.sh │ │ └── bw-mean.c │ ├── h5-mean.py │ └── h5-random.py ├── wes-creation.sh ├── wes-rand-acc.sh ├── wes-seq-acc.sh ├── wgs-creation.sh ├── wgs-rand-acc.sh └── wgs-seq-acc.sh └── figure5 ├── rnaseq ├── bedGraphToBigWig ├── build-suboptimal.zsh ├── build-uncompressed.zsh ├── d4-to-bigwig.sh ├── download.sh ├── find-high-expressed-region │ ├── Cargo.toml │ └── src │ │ └── main.rs ├── run-bigwig-parallel.sh 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