Svim

Changelog:
- Improve BND detection by detecting BNDs connecting opposite strands
- Add INFO:ZMWS tag to output VCF with number of supporting PacBio wells (enables filtering bad calls from only a few ZMWs)
- Add sequence alleles for INS (using the insertion sequence from a random supporting read)
- Add FORMAT:CN tag for tandem duplications
- Bugfixes

Changelog:
- add option `--sequence_alleles` to output sequence instead of symbolic alleles in VCF
- add option `--insertion_sequences` to output insertion sequences in VCF
- add option `--read_names` to output names of supporting reads in VCF

Changelog:
- Output breakends (BND) in VCF file
- Detect large tandem duplications even if they are not spanned by a single read (add flag `not_fully_covered`)
- Add new command line option to skip genotyping
- Make VCF output more flexible:
- Let user choose which SV types to include in VCF output
- Let user choose how to represent tandem and interspersed duplications (either as DUP or as INS)
- Add scatter plot of read support for reference and variant allele (see below)


Changelog:
- change default value for maximum distance in partitioning from 10kb to 1kb
- fix coordinates of BNDs (from 0-based to 1-based)
- fix sorting of VCF records
- add verbose mode which prints ignored partitions to log

Changelog:
- reduce memory consumption substantially

Changelog:
- add genotyping of translocation breakpoints (BNDs)
- bugfixes