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fix: ref does not match pileups in example

Alex Kanitz requested to merge fix-ref-example into main
  • Reference sequence in tests did not match the corresponding alignments, region and miRNA annotation files.
  • Update reference sequence, BGZIPped version, test output file and md5 sum of test output file
  • Add tabix dependency to generate BGZIPped reference to Conda environment file
  • Update documentation
  • No update to code

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