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v1.3.0

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@gordonkoehn gordonkoehn released this 12 Aug 08:02
· 60 commits to main since this release
v1.3.0
bac2f14

This release upgrades sr2silo to support SILO input format version 0.8.0, implementing a new JSON schema structure that flattens metadata fields to the root level and restructures genomic segments with explicit sequence, insertions, and offset fields.

Key changes:

in v1.2.0 pre

  • Migrated from nested JSON structure to flat schema with root-level metadata
  • Replaced padded alignments with offset-based positioning for better efficiency
  • Updated schema validation to distinguish between nucleotide and amino acid segments

in v1.3.0

The most significant change is making the LAPIS URL optional with intelligent fallback to default SARS-CoV-2 references (NC_045512.2) when LAPIS is unavailable or not specified.

  • Refactored reference genome handling to use fallback logic when LAPIS URL is not provided or fails
  • Made read_id a required field in the SILO schema with proper validation and positioning
  • Updated documentation and configuration files to reflect optional LAPIS URL usage
  • Improved file handling in the paired-end read merger to overwrite existing output files rather than raising an error, making workflows more robust.
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