Simplify input parameters

[timothymillar]

There are too many and some can be removed

Remove:

• [x] --sample-list
• [x] --ignore-base-phred-scores (altered to --use-base-phred-scores for now)

In the long term some arguments could be merged:

• [x] --bam, --bam-list, --sample-bam
• [x] --ploidy, --sample-ploidy
• [x] --inbreeding, --sample-inbreeding
• [x] --genotype-likelihoods, --genotype-posteriors: merged into a single --fields list?

[timothymillar]

Related, the new --sample-pool argument should also match this pattern with a single argument specify either a global pool of a file listing the pool of each sample