v1.8.0

• Add II-C2 and II-D to the database
• Rename Cas12f4 to V-M

v1.7.0

• Include new V-L: https://doi.org/10.15252/embr.202255481
• Update cutoffs for cas12e, cas12g, cas12j for increased sensitivity
• Update repeat model

v1.6.4

Fix bugs in BLAST for CRISPR, which made the program exit with an error at the write-gff stage

• BLASTed CRISPRs with spacers of length 0 are now discarded
• A faulty overlap check with minced CRISPRs is now fixed

v1.6.3

• MinCED options are now exposed to the user for fine-tuning CRISPR identification. CCTyper defaults are MinCED defaults.

v1.6.2

• Now also prints CRISPR and repeat/spacer coordinates in a GFF format
• Includes a new file as output when training repeatTyper, which contains probabilities for each prediction in the test set.

v1.6.1

Added undersampling when fitting repeatTyper model for a less biased model

v1.6.0

• New cutoffs for improved detection of V-F
• Addition of TnpB HMMs for competition against V-F HMMs
• New HMMs for improved detection of IV-C
• New HMMs to correctly discern between V-J (cas-phi) and V-K (CAST)
• New repeatTyper model with correct V-K/J repeats

For next version:

• Correct prediction of CAST (e.g. V-K) with large cargo

v1.5.1

Fix a CRISPR BLAST bug with 0-length spacers which happens if two repeats are found right next to each other

v1.5.0

• Fix problems with newer versions of pandas and xgboost
• Add length and GC content to repeatTyper models. RepeatTyper models before and after this version are incompatible

v1.4.4

Resolve conda issue with drawSvg pip dependency