Batch1: safe fixes with no alignment change (#219, #281, #261, #247, #240, #242) + noodles 0.116 - #289

Batch1: safe fixes with no alignment change (#219, #281, #261, #247, #240, #242) + noodles 0.116#289

Psy-Fer merged 2 commits into

mainscverse/rustar-aligner:mainfrom

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