.. BCCDC-PHL TB Genomics Database documentation master file, created by sphinx-quickstart on Thu Dec 15 16:15:13 2022. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. BCCDC-PHL FluViewer ========================================================== .. toctree:: :maxdepth: 2 :caption: Contents: Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` fluviewer.fluviewer =================== This module controls the overall flow of analysis by running each analysis stage. It runs the following analysis stages: 0. Read Normalization 1. Assemble Contigs 2. BLAST Contigs 3. Scaffolding 4. Read Mapping 5. Variant Calling 6. Consensus Calling 7. Summary Reporting .. automodule:: fluviewer.fluviewer :members: fluviewer.analysis ================== This module includes the steps required for each analysis stage. .. automodule:: fluviewer.analysis :members: fluviewer.database ================== This module includes functions used to check the integrity of the FluViewer database prior to analysis. .. automodule:: fluviewer.database :members: fluviewer.parsers ================= This module includes functions related to parsing output files. .. automodule:: fluviewer.parsers :members: fluviewer.report ================ This module includes functions related to building the final summary report. .. automodule:: fluviewer.report :members: fluviewer.plots =============== This module includes functions related to generating plots to visualize FluViewer outputs. .. automodule:: fluviewer.plots :members: fluviewer.cli_args =============== This module includes functions related to parsing and validating command-line arguments. .. automodule:: fluviewer.cli_args :members: fluviewer.logging_config =============== This module includes functions related to logging configuration. .. automodule:: fluviewer.logging_config :members: