v3.6-stable

What's Changed

• Updated index tool runs faster
• Fixed issue with frame shifts when only using MD tags
• Addressed issue with -g when only using contig name
• Changed Coverage-q30 column to just Coverage
• Fixed issue with --strand-correction used with --min-edits and ----min-read-depth that were not sufficiently filtered

Full Changelog: v3.5-stable...v3.6-stable

v3.5-stable

What's Changed

• Fixed issue with excluded regions - it works, and it's faster
• Changes --variants parameter default to "all"
• Updated --strand options and output to match REDI2
• Fixed bug from fasta file ref where reference base was sometimes a string and not a list
• Added DNA annotation tool from REDI2
• Temporary file location can now be defined with --temp-dir parameter

v3.0-alpha

What's Changed

• Moved some reditools methods to a utilities script by @ahanden in #1
• Exclude genomic regions by @ahanden in #2
• Code cleanup by @ahanden in #5
• Dev by @ahanden in #16

Full Changelog: https://github.com/BioinfoUNIBA/REDItools3/commits/v3.0-alpha