├── .editorconfig ├── .gitattributes ├── .gitignore ├── .travis.yml ├── Dockerfile ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── PKG-INFO ├── README.rst ├── README_pypi.rst ├── automate_chronqc ├── CONFIG │ ├── JSON │ │ ├── CET_config.json │ │ ├── NGS_config.json │ │ └── PCR_config.json │ └── crongen_config.ini ├── README.rst └── test.ini ├── chronqc ├── __init__.py ├── _version.py ├── chronqc.py ├── chronqc_annotation.exe ├── chronqc_annotation.py ├── chronqc_crongen.py ├── chronqc_db.py ├── chronqc_plot.py ├── config │ ├── CET_config.json │ ├── NGS_config.json │ ├── PCR_config.json │ ├── chronqc.conf │ └── crongen_config.ini ├── db │ └── chronqc.annotations.db ├── dev.py ├── templates │ ├── absolute_threshold.txt │ ├── bar_line_plot.txt │ ├── base_template.html │ ├── box_whisker_plot.txt │ ├── html.txt │ ├── mean_and_stdev.txt │ ├── percent_plot_threshold.txt │ ├── sidebar.txt │ └── stacked_bar_plot.txt └── utils.py ├── docs ├── Makefile ├── _static │ ├── ChronQC_logo.png │ ├── ChronQC_workflow.png │ ├── style.css │ ├── timeseries_absolute_threshold.png │ ├── timeseries_bar_line.png │ ├── timeseries_box_whisker.png │ ├── timeseries_mean_n_stddev.png │ ├── timeseries_percentage_category.png │ ├── timeseries_percentage_samples_abv_threshold.png │ └── timeseries_stacked_bar.png ├── _templates │ └── layout.html ├── automate_chronqc.rst ├── chronqc.rst ├── chronqc_setup.rst ├── citation.rst ├── conf.py ├── faqs.rst ├── index.rst ├── plots │ ├── plot_options.rst │ ├── time_series_with_bar_line_plot.rst │ ├── time_series_with_stacked_bar_plot.rst │ ├── timeseries_absolute_threshold.rst │ ├── timeseries_box_whisker.rst │ ├── timeseries_mean_n_stddev.rst │ ├── timeseries_percentage_category.rst │ └── timeseries_percentage_samples_abv_threshold.rst └── run_chronqc.rst ├── examples ├── custom_db_example │ ├── PCR_config_demo.json │ ├── chronqc_custom_PCR_db.sqlite │ ├── chronqc_custom_db.sqlite │ ├── config.json │ └── readme.md ├── multiqc_example_1 │ ├── multiqc_data │ │ ├── multiqc_fastqc.txt │ │ ├── multiqc_general_stats.txt │ │ ├── multiqc_report.html │ │ └── multiqc_sources.txt │ ├── readme.md │ ├── run_date_info.csv │ └── sample.json ├── multiqc_example_2 │ ├── readme.md │ ├── sample.json │ ├── year_2016 │ │ ├── multiqc_data │ │ │ ├── multiqc_bamtools_stats.txt │ │ │ ├── multiqc_bcftools_stats.txt │ │ │ ├── multiqc_fastqc.txt │ │ │ ├── multiqc_general_stats.txt │ │ │ ├── multiqc_peddy.txt │ │ │ ├── multiqc_samtools_flagstat.txt │ │ │ ├── multiqc_samtools_idxstats.txt │ │ │ └── multiqc_sources.txt │ │ └── run_date_info.csv │ └── year_2017 │ │ ├── multiqc_data │ │ ├── multiqc_bamtools_stats.txt │ │ ├── multiqc_bcftools_stats.txt │ │ ├── multiqc_fastqc.txt │ │ ├── multiqc_general_stats.txt │ │ ├── multiqc_peddy.txt │ │ ├── multiqc_samtools_flagstat.txt │ │ ├── multiqc_samtools_idxstats.txt │ │ └── multiqc_sources.txt │ │ └── run_date_info.csv └── readme.md ├── install-files.txt ├── requirements.txt ├── 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