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This reverts merge request !5

Update script to make SNP caller commands: add command line options to pass to caller & mpileup.

See merge request !5

Conflicts:
	src/computeGenomeCoverage.py

DOC Spell check comments

See merge request !6

This code has fewer repetitions and is more readable

- minimum coverage (“-c”, default 4)
- minimum threhold (“-t”, default 4)
- minimum frequency (“-p”, default 0.01)
- maximum depth per position and sample for mpileup (“-d”, mirroring mpileup -d option, default 20,000)
- rename debugging option from “-d” to “-D”

Make thresholds command line options instead of hard coded

Also:
- Fix a crash when -i option is missing
- Add Makefile dependency

See merge request !4

Provide a warning to the user instead.

Remove unused function

See merge request !3

Improve documentation

See merge request !2