Earl Grey v4.2.2

What's Changed

• Version 4.2.0 - Increased Efficiency and Patch Fixes by @TobyBaril in #101
• 102 bug when using soft link to genome by @TobyBaril in #103

Full Changelog: v4.1.1...v4.2.2

Earl Grey v4.2.1

• Small patch fixes and preparations for pandas 3.0

Earl Grey v4.2.0

• Removed inefficient for loop in final repeat merge step
• updated overlap algorithm to handle nested insertions
• new divergence calculator! This now works on the final merged repeats file and calculated kimura 2-parameter distance
• new plots! new divergence calculator now produces new plots. Same idea - TE landscape, but now with two more plots showing landscapes by TE classifications for more indepth analyses.

Earl Grey v4.1.1

• Patches to TEstrainer processing to resolve SSR detection

Earl Grey v4.1.0

• Updates to the final GFF annotation file to highlight the tool used
• Various updates to the README and documentation

Earl Grey v4.0.8

• Recoded the filtering of overlapping repeats using Dplyr to increase speed and efficiency. Gone are the inefficient for-loops!

Earl Grey v4.0.7

• Small patches to increase the parameters available to users to fine-tine the BEAT process
• It is now possible to specify the number of sequences to be used in TE consensus generation (default 20), the number of flanking bases to be added each time (deafault 1000bp), and the maximum number of BEAT iterations to run (default 10).

Earl Grey v4.0.6

• Patch to add failsafes in case all known repeats are hardmasked by the initial RepeatMasker run, which previously caused TEstrainer to fail.
• A warning is now pushed to the log in case this behaviour is not expected by the user.
• Beware of using small subsets for testing, it is unlikely RepeatModeler2 can find repetitive DNA in tiny portions of test sets!

Earl Grey v4.0.5

Patch creation of dictionary.

Earl Grey v4.0.4

Small patch in intitial genome preparation. No change in analysis outputs from previous version.