Genomic improvements

[mytkom]

Improvements:

1. Handling of unpaired sequences.
2. Add CLI option to treat sequences that overflow out of the amplicon of a small number of bp as included in this amplicon (-f, --amp-overflow).
3. Filter by alignment ratio (ratio of bps aligned correctly with reference genome), AS tag / seq_length (or sum of sequence length for paired-end sequences).
4. Use AS score as quality from now---not MAPQ score like before.

[mytkom]

I now wonder if I should add those new fields to the Read struct. It is really readable code now, but at the same time, algorithms wouldn't use the new fields, so the only place it is needed is in the bam_api::BamApi class during preprocessing. So then maybe I should move it to vectors there to save RAM? What do you think? @migoox @plebania @Willu12