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add microbial mode #6694

Merged
merged 18 commits into from
Aug 2, 2021
Merged

add microbial mode #6694

merged 18 commits into from
Aug 2, 2021

Commits on Mar 19, 2021

  1. rebased version of this code

    @jamesemery @ahaessly
    jamesemery authored and ahaessly committed Mar 19, 2021
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  2. fixed an issue where the logic for suffix ends was incorrect for dang… 

    …ling tails
    @jamesemery @ahaessly
    jamesemery authored and ahaessly committed Mar 19, 2021
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  3. responding to review comments

    @jamesemery @ahaessly
    jamesemery authored and ahaessly committed Mar 19, 2021
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  4. manual rebase

    @ahaessly
    ahaessly committed Mar 19, 2021
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  5. change misspellings of dangling to the correct spelling

    @ahaessly
    ahaessly committed Mar 19, 2021
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  6. remove change from bad merge

    @ahaessly
    ahaessly committed Mar 19, 2021
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  7. parent 6d43103 

    author Andrea Haessly <[email protected]> 1582141271 -0500
committer Andrea Haessly <[email protected]> 1611852899 -0500

parent 6d43103
author Andrea Haessly <[email protected]> 1582141271 -0500
committer Andrea Haessly <[email protected]> 1611852778 -0500

initial impl
tested shift and chain
make offset optional
fix format of chain file
make offset optional
fix format of chain file
add interval output
    @ahaessly
    ahaessly committed Mar 19, 2021
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  8. check for is empty

    @ahaessly
    ahaessly committed Mar 19, 2021
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  9. add test, update from PR

    @ahaessly
    ahaessly committed Mar 19, 2021
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Commits on Mar 22, 2021

  1. update from PR

    @ahaessly
    ahaessly committed Mar 22, 2021
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Commits on Apr 1, 2021

  1. update from PR

    @ahaessly
    ahaessly committed Apr 1, 2021
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Commits on Jul 21, 2021

  1. update documentation

    @ahaessly
    ahaessly committed Jul 21, 2021
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  2. add pruner fix

    @ahaessly
    ahaessly committed Jul 21, 2021
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  3. remove unfinished code

    @ahaessly
    ahaessly committed Jul 21, 2021
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  4. test microbial mode

    @ahaessly
    ahaessly committed Jul 21, 2021
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  5. fix bug

    @ahaessly
    ahaessly committed Jul 21, 2021
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Commits on Jul 27, 2021

  1. this changes the behavior of the adaptive pruner at low/patchy refere… 

    …nce coverage sites\nAdd large files to resources
    @ahaessly
    ahaessly committed Jul 27, 2021
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Commits on Jul 29, 2021

  1. doc as beta feature

    @ahaessly
    ahaessly committed Jul 29, 2021
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