Fix chain plotter crash from empty blocks

SVTopo

• Version bump

SVTopoVz

• Fix crash from bug introduced in v0.1.2

Fix segfault issue with some bams

SVTopo

• Fixes an instability where some BAMs led to a segmentation fault due to negative indices of chromosome names

SVTopoVz

• Minor fix for ordering of multi-segment inversion blocks

Remove unstable URL option for exclude regions

SVTopo

• Removes the URL option for exclude regions bed file as it proved unstable across different platforms.
• Adds filter for phase consistency in reads connecting same-chromosome breakends: if alignments connecting two breakends are tagged from different phasesets or haplotypes they are dropped. This does not apply to connections formed from VCF calls.
• Drops max size for same-chromosome connections

SVTopoVz

• Unchanged

vcf-supported version

SVTopo

• Adds support for sawfish VCF to improve variant identification accuracy with the new --supporting-reads and --vcf.
• Simplifies user interface by removing the following:
  • --quiet
  • --allow-unphased
  • --no-filter
• Changes the --prefix to the simpler option --json-out
• Adds the --exclude-regions argument as a required bed file for region exclusion.

SVTopoVz

• Changes --log-level to --verbose for consistency with svtopo.
• Alters the exclusion of simple variants to default by changing the --ignore-simple-dels and --ignore-simple-dups to --include-simple-dels and --include-simple-dups, respectively.

SVTopoVz split view

This release includes a split-view option for extra-large genomic regions. It is intended to shortly provide support for multi-chromosomal rearrangements.

This release also adds some minimal changes to the plotting view:

• Legend with block sizes
• Sample chain plot in normalized sizes instead of proportional
• Extra reference chain plot at the bottom in normalized sizing

The SVTopoVz interface now allows filtering on best-guess variant types DEL and DUP. This option has been dropped from SVTopo.

• DEL: two forward spanned blocks, one forward unspanned
• DUP: two forward spanned blocks, one reverse unspanned

Initial release

First HiFi-SVTopo release, with rust binary for BAM parsing and python source code for generation of complex SV plots.