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Update to the depth filtering for mpileup. #1084

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Commits on Jun 15, 2020

  1. Update to the depth filtering for mpileup.

    We can now count the depth anywhere along the read rather than only at
    the left end.  It's not buffering reads up so it doesn't know what's
    about to come, so for any individual column it'll still favour reads
    that end near a column than start near a column, but by counting at
    the right hand end we avoid the boom & bust approach to before where
    the coverage could plumet to zero immediately following a large spike.
    
    With iter->depth_pos = 1.0 the coverage ends up being a minimum of
    maxcnt (assuming the true coverage is higher), rather than a maximum
    of maxcnt.  So we go over-depth, but avoid the drop outs.
    jkbonfield committed Jun 15, 2020
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Commits on Jun 16, 2020

  1. Revised the necessity to only remove duplicates with identical start

    coord.  It's not so vital with the revised formula, so within 10 works
    good enough and prevents some more excessive depth raises.
    
    Also (ifdef-ed out) implemented the "other" more complex method, for
    comparison.  Cull whichever we wish before merging.
    jkbonfield committed Jun 16, 2020
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