Update script to make SNP caller commands: add command line options to pass to caller & mpileup.
This commit allows to pass command line options through the bash script metaSNP_SNP directly to the caller and to mpileup. The following options are introduced:
- 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”