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pre-alignment collate options #268

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pre-alignment collate options #268

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Commits on Mar 4, 2020

  1. add selection of pre-alignment collate methods (simple collation not … 

    …enough for realignment of coordinate-sorted input)
    @dozy
    dozy committed Mar 4, 2020
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  2. move initial collate step upstream (allows subssampling to be retaine… 

    …d in realignment)
    @dozy
    dozy committed Mar 4, 2020
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  3. extend port extraction in command arrays to recursively check inside … 

    …elements which are themselves arrays
    @dozy
    dozy committed Mar 4, 2020
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  4. extend samtool -F filter to remove supplementary reads before subsamp… 

    …ling (for realignment)

add informational messages showing reads_count and calculated frac to log (stderr output)
    @dozy
    dozy committed Mar 4, 2020
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Commits on Dec 4, 2021

  1. Merge branch 'devel' into pa_collate_options

    @dozy
    dozy committed Dec 4, 2021
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