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Fixes for -min and -max parameters#234

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lcoombe merged 4 commits intomasterfrom
fix_min_max
Oct 9, 2024
Merged

Fixes for -min and -max parameters#234
lcoombe merged 4 commits intomasterfrom
fix_min_max

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@lcoombe lcoombe commented Oct 9, 2024

  • Genome and metagenome modes: Add extra check before writing read to file to avoid reads that are slightly out of the specified length range
    • Same for unaligned reads
  • Clarified in the transcriptome help page that -min and -max are only used for unaligned reads (min_len and max_len options. #160)
  • To be consistent with genome mode, don't allow --perfect and --chimeric reads simultaneously in metagenome mode

…E.md

- Clarify that the -min and -max parameters in transcriptome mode are ONLY used for unaligned read simulation
- counter-intuitive to have chimeric reads in perfect mode
- This update is consistent with genome mode
@lcoombe lcoombe requested a review from parham-k October 9, 2024 19:21
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Looks good. Thanks @lcoombe.

@lcoombe lcoombe merged commit 54a49aa into master Oct 9, 2024
@lcoombe lcoombe deleted the fix_min_max branch October 9, 2024 21:13
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