v1.11.0

Changed

• Add an additional whatshap haplotag process after the final VCF phasing.
• Updates to the phasing subworkflow significantly impact the runtime and storage requirement for the workflow, as detailed here.
• Several performance improvements which should noticeably reduce the running time of the workflow

Fixed

• Updated the version of Straglr, which addresses the following:
  • Repeats can now be called in RFC1
  • Start position of called STRs is 1-based rather than 0-based
  • VCF headers now match those in the FORMAT field
• Generate allChromosomes.bed using samtools faidx index instead of pyfaidx, to avoid a KeyError
• Inconsistent file ownership of bundled Clair3 model files which could lead to subuid errors in some environments