Inline conversion optimization (#186)

* add compression for output fasta
* add gz to fasta
* change cli to remove inputs as options
* update rule to match new cli
* update summary for new api
* rm redundant required= from argparse
* add this for dev reasons
* replace execute() with executemany()
replace manual reader with pysam FASTX
* safety measure for really short seq
* fix seq length test

harpy/bin/inline_to_haplotag.py

@@ -130,3 +130,4 @@ def process_record(fw_rec, rv_rec, barcode_database, bc_len):
             rv_out.write(new_rv.encode("utf-8"))
 
 bc_db.cursor().close()
+