Svim

Changelog:

- adds consensus sequence computation for insertions
- improves clustering step:
- considers sequence similarity when clustering insertions
- prevents signatures from same read to be clustered together
- outputs sequence alleles for all SV types except BNDs and DUPs by default
- updates default parameters
- bugfixes

Changelog:
- fix invalid start coordinates in VCF output
- issue warning for invalid characters in contig names

Changelog:
- improve clustering of translocation breakpoints (BNDs)
- improve --all_bnds mode
- bugfixes

Changelog:
- fix and improve clustering of insertions (fix bugs introduced in v1.3.1)
- add option `--all_bnds` to output all SV classes in breakend notation
- update default value of `--partition_max_distance` to avoid very large partitions
- various bugfixes

Changelog:
- Small changes to partitioning and clustering algorithm
- Add two new command-line options to output duplications as INS records in VCF
- Remove limit on number of supplementary alignments
- Remove q5 filter
- Bugfixes