Release 0.5.4 · akikuno/DAJIN2

💥 Breaking

Use simulated annealing to optimize cluster assignments in clustering.constrained_kmenas [Commit Detail]
- Since ortools is not installable on osx-arm64 in Bioconda, I implemented an alternative method, simulated annealing, to solve min_cost_flow.
Change the criteria for terminating clustering. [Commit Detail]
- The following termination criteria have been added:
  - Minimum cluster size is less than or equal to 0.5% of the sample's read number.
  - Decrease in the proportion of samples with a silhouette score of 0.25 or higher.
- The following termination criterion has been removed:
  - Adjusted Rand Index >= 0.95, as it led to early termination when minor clusters were generated.
The threshold for clustering.strand bias determination has been loosened. [Commit Detail]
- This adjustment addresses cases like +:13, -:2 (0.87) observed in example_flox/flox-1nt-deletion.
- Since the minor allele is particularly susceptible, further adjustments may be necessary in the future.