v1.4.2

Update plot engine to output vector graphics (svg) along with png plots, along with other aesthetic updates.

v1.4.1

• Include the new Cas13X and Cas13Y as VI-X and VI-Y subtypes
• Update to the newest repeatTyper model

v1.4.0

• Include CRISPR detecting by BLASTing known repeats near cas operons for a more sensitive CRISPR detection
• Inlude the updated repeatTyper model instead of the one based on the curated database.

v1.3.0

• Include strand information of the cas operons
• Numeric fasta headers are now fixed instead of aborting
• Speed-up CRISPR stats part for long CRISPR arrays by approximation. This can be by-passed with --exact_stats

v1.2.4

• Update names of a few HMMs in line with recent research
• Fix bug popping up with newer pandas version

v1.2.3

Add HMMs for new V-A variants described here: https://www.liebertpub.com/doi/10.1089/crispr.2020.0043

v1.2.1

• Fix an edge case bug where some single effector cas operons were falsely denoted as Ambiguous, despite unambiguous typing
• Loosen cutoffs on Cas12a to get a more sensitive V-A prediction

v1.2.0

• Add CRISPR stats: Repeat identity, spacer identity, repeat length, spacer length, spacer length standard error
• Add a CRISPR filtering step based on the stats. CRISPRs are only trusted if:
  • repeat identity is high (>70%),
  • spacer identity is low (<55%),
  • spacer length standard error of the mean is low (<3.5).
  • CRISPRs adjacent to cas operons are always retained,
  • CRISPRs with a subtype prediction probability > 0.9 are always retained.
• Fix a plotting bug for sequences without any match to a Cas HMM
• Fix a redo-ing bug for sequences without any match to a Cas HMM

v1.1.5

Expand subtypes into variants:

• V-B into V-B1 and V-B2
• V-F into V-F1, V-F2, V-F3, and the remainder in V-F
• VI-B into VI-B1 and VI-B2

v1.1.3

Add the possibility to run HMMER against a custom HMM database. Names of matches will be added to the previously unknown (non-cas) ORFs in the plot