Codestin Search App

Release version v1.1.7
Add extra check in overlap mode
- If estimated overlap trim on either sequence is greater than the length of the other, do not trim

Release version 1.1.6
Fix to overlap mode - in certain edge cases, the trimming coordinates could be invalid
- With this fix, if this is detected, fall back to no trimming for the particular scaffold(s) involved
Documentation updates

Release version 1.1.5
Fix for cases where no scaffolding was seen for circular references (#113)
- With fix, circular graphs are detected and properly used for scaffolding sequences
Documentation update - ensure that any terminal N's in sequences are removed prior to ntJoin

Release version v1.1.0
Introduces new 'overlap' feature, which is enabled by default (overlap=True)
- For adjacent sequences that have a putative overlap based on gap distance estimates:
  - Compute minimizers with a lower k and w (to increase sensitivity), and create an undirected minimizer graph using minimizers found in the putative overlap region (in multiplicity of 1 in both sequences)
  - Use the minimizer graph to anchor the sequences to each other, and use the coordinates to trim the overlapping sequence
- This feature reduces the incidence of local misassemblies and duplications, created when overlapping sequences are naively joined end-to-end
Update btllib to v1.4.4
General bugfixes and documentation updates

Releases: BirolLab/ntJoin