Svim

Changelog:
- Replace graph-based clustering (using maximal cliques) with hierarchical clustering
- Modify scoring function so that the number of signatures in a cluster gains importance
- Improve partitioning prior to clustering
- Improve calling from coordinate-sorted SAM/BAM files
- Improve VCF output:
- add SUPPORT INFO field
- add FILTER q5 for variants with score <5
- remove old FILTERs q20 and q30 (obsolete because of new scoring)
- sort VCF output naturally (e.g. chr10 behind chr2)

Changelog:

- bug fixes (8, 10)
- included exception message into log files
- removed unused code
- added tests and set up Travis

Changelog:
- add support for coordinate-sorted SAM/BAM files
- improve VCF output and increase compatibility with IGV and truvari
- fix: erroneous removal of insertion candidates

Changelog:

- refactor alignment pipeline to make it more robust against failures:
- use run(.., shell=True) instead of Popen(stdout=PIPE)
- add check whether alignment tools are installed before starting pipeline
- catch exceptions properly
- pipe gzipped files into gunzip instead of writing out uncompressed file

Changelog:

- **feature**: merge the following two SV classes: interspersed duplication and cut&paste insertions
- **feature**: add flag to interspersed duplications indicating whether genomic origin might be deleted (cut&paste event)
- check whether input BAM is query-sorted
- update README
- include LICENSE file into package

Changelog:

- **feature**: add minimap2 to built-in aligners
- **feature**: restructure repository to conform to Python package structure
- require translocation breakpoints on both sides of a deletion to yield a cut&paste insertion
- ensure interspersed duplication signatures have positive size (bugfix)
- fix wrong SV type in BED output (bugfix)