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LRAA Release v0.12.0

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@brianjohnhaas brianjohnhaas released this 14 Nov 13:23
· 320 commits to main since this release
LRAA_v0.12.0
ed6cea8

v0.12.0, November 14, 2025

  • caching initially constructed splice graphs for reuse in downstream quants to avoid reconstruction effort.
  • all splice graphs for all steps leverage the normalized read coverage (not just isoform ID)
  • added --num_parallel_contigs to control contig-level concurrency (default 4 workers); --num_threads_per_worker (legacy --CPU alias) specifies cores allocated per contig/strand worker (default 1 core)
  • default --oversimplify now targets mitochondrial contigs ("chrM,M")
  • wdls optimized for splitting data per chromosome
  • scatter runs per chromosome only (strand-level splitting removed) with subjobs shuffled for improved load balancing
  • including ref-annot gene symbol integration into single cell pipeline
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