├── .gitignore ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── graphs ├── Benchmark.py ├── bedgraph_stats.csv ├── find_stats.py ├── generate_graphs.py ├── make_benchmarks.py ├── runHelix.pbs ├── run_benchmark.sh ├── v-1_graphs │ ├── ENCFF050CCI │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF321FZQ │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF376VCU │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ ├── run_time_results.txt │ │ ├── values_indexed.png │ │ └── values_indexed.txt │ ├── ENCFF384CMP │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF631HEX │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF643WMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF770CQD │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF847JMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ └── format_results.sh ├── v1_graphs │ ├── ENCFF050CCI │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF321FZQ │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF376VCU │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF384CMP │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF631HEX │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF643WMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF770CQD │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ └── ENCFF847JMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt ├── v2_graphs │ ├── ENCFF050CCI │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF321FZQ │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF376VCU │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF384CMP │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF631HEX │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF643WMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF770CQD │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ └── ENCFF847JMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt └── v3_graphs │ ├── ENCFF000KYT │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF000LAB │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF050CCI │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF321FZQ │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF376VCU │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF384CMP │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF631HEX │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF643WMY │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF726XVA │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF770CQD │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF847JMY │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF877IHY │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ └── runtime_table.png ├── pyBedGraph ├── BedGraph.py ├── Chrom_Data.py ├── Chrom_Data_Complete.py ├── __init__.py ├── ignore_missing_bp.c ├── ignore_missing_bp.pyx ├── include_missing_bp.c ├── include_missing_bp.pyx ├── util.c └── util.pyx ├── setup.py └── test ├── default.conf ├── extensive_test.py ├── make_test_files.py ├── run_tests.sh ├── test.py └── test_files ├── README.py ├── custom_intervals.txt ├── hg38.chrom.sizes ├── mm10.chrom.sizes ├── myChrom.sizes ├── random_test.bedGraph ├── random_test.bigWig └── test_intervals.txt /.gitignore: -------------------------------------------------------------------------------- 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