Redo extraction of charging values

[jayhesselberth]

Closes #45

Uncovered an issue wherein a small number of reads have >= 1 value for ML (charging tag). Not sure why that is, but for now we ditch them (it was < 10 reads for a large run).

Split get_final_bam_and_charg_prob into 2 rules:

1. transfer_bam_tags
2. get_cca_trna

Replace the awk / sed strategy of extracting chargin values with a python script.