PanGeTools

• Added Seqwish v0.7.9
• Updated VG to v1.58.0
• Beta testing wfmash v0.16.0
• Updated GFAvc to v0.4

Anchors2Path.py

Simple script to search and retrieve all anchor nodes (nodes traversed once and only once by all haplotypes/paths in the graph). The intended use is to extract a subgraph between two anchor nodes and preserve all variability.

GFAvc v0.4

Changelog :

• Added support for gzipped GFA
• Stripping escape character when parsing
• Added GFA1.0 to GFA1.1 conversion direction (intended for PGGB GFA)
• Optional index can be passed to add START-END range to walks when converting from GFA1.0 to GFA1.0

Note on GFA1.0 to GF1.1 conversion : As PGGB has no reference, every sample is set as reference (i.e. added to the space separated list from the GFA header under RS:Z:...). This simplify the use of VG tools such as vg surject which only surject onto reference walks. This also prevent paths/walks from having different names between vg and non-vg file format (no phase_block)