Csstar

Added:
- new `--ungapped` option to invoke ungapped BLASTn alignment (default off, remains same as before)

Changed:
- fixed bug so now tmp space is used for temporary `makeblastdb` files

Added:
- automatically detects input file format from filename; now allows GunZip compressed GenBank and FastA
- `blastn` system call by default uses all CPUs available
- minimum alignment fraction default unchanged (40%) but new `--aln-fraction` option allows a user to change the threshold
- tests input argument values are within relevant ranges
- summary tab-delimited report default unchaged (stdout) but new `--report` option to specify outfile
- new option to verify input genome is nucleotide composition with `--min-ACGT`
Changed:
- `--similarity` option removed and replaced with `--identity` option with same default (95%)
- clarified data fields parsed by converting lists to dictionary
- camelcase of variable names removed, no longer following the Java vars written for the SSTAR GUI
- PEP8 compliant according to flake8 tests

Added:
- opt to print version number
- opt to provide the output file's basename
- new feature that identifies truncated porins and AR gene determinants

Revised:
- readme file to explain filtering output for full-length variant identification and for discovering non-functional (truncated) porin sequences

`c-SSTAR.py` generates output that `SSTAR.jar` produces from Tom's [most recent commit](https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance-SSTAR-/commit/52aff8108fe31b4c86380421e7209d3858afd8cf) with two exceptions:
- the best match for redundant AR variants are reported; [issue reported](https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance-SSTAR-/issues/1)
- all hits that meet the threshholds described in the SSTAR manuscript are reported [issue reported](https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance-SSTAR-/issues/2)