Document output parameters AMS/af-AMS

[PierreLaville]

Improve naming consistency for parameters in output files:

• aams_run_tables: test_pair_test_run_pep_df_mindp_20_maxdp_400_minad_5_gq_20_thresh_0.8_bl_3.pkl
• run_tables: test_pair_test_run_mismatches_20_400_5_gq_20_0.8_bl_3.tsv

Or log parameters in a specific file.

[PierreLaville]

Furthermore, in the example above the thresh parameter (0.8) uses the . character which could lead to some issues (confusion with file extension, harder parsing with regular expressions, etc.), so should be avoided.

[huguesrichard]

Indeed, we can go on two different way:

1. keep the parameters in the file name. In this cases there should be a function that is taking care of preparing the parameters string to plug into the filename

2. use a log file with the same extension as the output file (or main directory) and with some lines listing all the parameters.

I prefer when the file creations are explicitly asked by the user, so I would vote in favor of solution 2. (with solution 1. the file creation is implicit as a function of the run parameters).

The problem with the float parameter 0.8 for the threshold also votes in favor of solution

[PierreLaville]

As discussed, option 2. also enhances reproducibility (keeping track of which command has been run on which file). See Logging module in Python.