v2.1.0

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

v2.0.0

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

c-SSTAR_v1.2

c-SSTAR_v1.2

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_v1.0

v1.0 c-SSTAR release

c-SSTAR.py generates output that SSTAR.jar produces from Tom's most recent commit with two exceptions:

• the best match for redundant AR variants are reported; issue reported
• all hits that meet the threshholds described in the SSTAR manuscript are reported issue reported