Add Coverage Statistics Calculation Script for Mosdepth

[bshifaw]

This pull request introduces a new script to calculate coverage statistics from Mosdepth output files. The script processes coverage values, calculates various summary statistics, and outputs the results in a JSON file.

Argument Parsing:
Command-line arguments for input file, coverage column, output prefix, rounding precision, and debug mode.

Statistics Calculation:
Calculation of mean, quartiles, median, interquartile range, standard deviation, mean absolute deviation, percentage of coverage values above 4x, and evenness score.
JSON Output: Write the calculated statistics to a JSON file.

Changes:
Added docker/lr-mosdepth/coverage_stats.py with functions for argument parsing, file handling, and statistics calculation.

coverage_stats.py script
Example log:

> python /Users/longreadpipes/docker/lr-mosdepth/coverage_stats.py  --cov_col 4 --round 2 --output_prefix test_example.coverage_over_bed test_example.text  

INFO:root:Arguments: Namespace(mosdepth_regions='test_example.text', cov_col=4, output_prefix='test_example.coverage_over_bed', round=2, debug=False)
INFO:root:Calculating coverage statistics
INFO:root:Opened file: test_example.text
INFO:root:Percentage of coverage values greater than 4x: 1.0
INFO:root:Evenness score: 0.92
INFO:root:Summary statistics: {'mean_cov': 16.0, 'q1_cov': 15.0, 'median_cov': 16.0, 'q3_cov': 17.75, 'iqr_cov': 2.75, 'sstdev_cov': 3.69, 'mad_cov': 2.67, 'percent_above_4x': 1.0, 'evenness_score': 0.92}
INFO:root:Writing summary statistics to file: test_example.coverage_over_bed.cov_stat_summary.json

Example output file

> cat test_example.coverage_over_bed.cov_stat_summary.json  

{"mean_cov": 16.0, "q1_cov": 15.0, "median_cov": 16.0, "q3_cov": 17.75, "iqr_cov": 2.75, "sstdev_cov": 3.69, "mad_cov": 2.67, "percent_above_4x": 1.0, "evenness_score": 0.92}