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Use read pairing information in kneaddata_bowtie2_discordant_pairs #16

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Use read pairing information in kneaddata_bowtie2_discordant_pairs #16

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Commits on Feb 16, 2021

  1. Run bowtie2 multiple times in kneaddata_discordant_pairs and --reorder 

    which avoids the problem of having to pair up the reads afterwards
so the memory usage doesn't depend on the input size

Add more logging, turned on after the --verbose option (if not verbose, print only the counts, as before)

Add --bypass-trf for unit tests that are meant to be bowtie2 only
    @wbazant
    wbazant committed Feb 16, 2021
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Commits on Jul 27, 2021

  1. Allow for a file less than 100 lines

    @wbazant
    wbazant committed Jul 27, 2021
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Commits on Nov 4, 2022

  1. Adding argument for specifying if mates are equal or different

    @rdemko2332
    rdemko2332 committed Nov 4, 2022
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  2. Changing value error message

    @rdemko2332
    rdemko2332 committed Nov 4, 2022
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  3. Adding query_mate_separator option, no logic for finding queryId and … 

    …mate
    @rdemko2332
    rdemko2332 committed Nov 4, 2022
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  4. Improving error messages

    @rdemko2332
    rdemko2332 committed Nov 4, 2022
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