CONTRIBUTING.md

Contributing to Post-Processing

1. Follow README.md for package setup.

2. Determine the file type that you'd like to add a post-processing operation. You can run pv --help to see supported file types.

3. If the file type exists, for example maf, add the operation as a command for that file type. You can run pv <filetype> --help to see available commands.

4. If the command doesn't require sub-commands, for example pv maf <command>, you can simply add a new command block to postprocesssing_variant_calls/<filetype>/main.py:

   #TODO change command name and help
   @app.command(
       "germline_status", help="Tag a variant in a MAF file as germline based on VAF value"
   )
   #TODO change command function name 
   #TODO change argument names
   def germline_status(
       maf: Path = typer.Option(
           ...,
           "--maf",
           "-m",
           exists=True,
           file_okay=True,
           dir_okay=False,
           writable=False,
           readable=True,
           resolve_path=True,
           help="MAF file to subset",
       ),
       output_maf: Path = typer.Option(
           "output.maf", "--output", "-o", help="Maf output file name."
       ),
       separator: str = typer.Option(
           "tsv",
           "--separator",
           "-sep",
           help="Specify a seperator for delimited data.",
           callback=check_separator,
       ),
   ):
       #TODO change file class to 
       # prep maf
       mafa = MAFFile(maf, separator)
       #TODO change file type operation 
       #TODO you will need to add the operation(s) as a method to the file's class
       mafa = mafa.tag("germline_status")
       #TODO change file writing to handle expected type
       mafa.to_csv(f"{output_maf}".format(outputFile=output_maf), index=False, sep="\t")
       return 0
   
   

   After adding the block you will need to resolve the TODOs in the code block.

   The most important of these is adding your operation as a method to the file's class.

   The file's class can be found in: postprocesssing_variant_calls/<filetype>/helper.py.

   If you are un-familiar with classes and methods you may need to read: https://www.w3schools.com/python/python_classes.asp.

5. If the command does require sub-commands, for example pv maf <command> <sub-command>, you must add a new process script under a new sub-command folder.

   To do this run:

   mkdir postprocessing_variant_calls/<filetype>/<command>
   touch postprocessing_variant_calls/<filetype>/<command>/__init__.py
   cp postprocessing_variant_calls/data/method_process.py postprocessing_variant_calls/<filetype>/<command>/<command>_process.py
   

   Then, create your sub-commands by completing the TODOs noted in `method_process.py``.

   There also may need to be additional changes depending on the requirements of the new operation such as adding helper functions. These can be added to postprocessing_variant_calls/<filetype>/helper.py

   Lastly, you will need to add this block to the top of postprocessing_variant_calls/<filetype>/main.py:

   from .<command> import <command>_process
   app.add_typer(<command>_process.app, name="<command>", help="<command_help>")
   

   Note: the new command is specified by the block added to the postprocessing_variant_calls/<filetype>/main.py. While the sub-commands are specified in the copy of method_process.py.

6. If the file type does not exist, you must create a new class for the file type. Please reach out to @buehlere if this type of feature is needed.