remove assembly.py and replace with bwa.py
add TODO re: which command for python
remove redundant code now in phyluce/bwa.py
move magic fastq raw-read finding code to its own module
create coverage calculator for trinity assemblies (can expand to other assemblies later)
given ability to compute trinity assembly coverage, compute coverage across UCE loci
Make all options flags and set to required to reduce confusion on CLI
flesh out help messages
change coverage and identity to min-coverage and min-identity
Add flags for all parameters, add more help info.
add periods to end of all help statments
standardize parameters and add periods to all help statements
standardize parameters, add required flags for all, flesh out help, add periods to all help statements
return number of missing loci per taxon instead of decrease by taxon
fix typos
add logging
add logging
add logging
adding logging module
make db and contig attribute names  more generic