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Remove the mpileup BAM_CREF_SKIP filter. #2281

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Remove the mpileup BAM_CREF_SKIP filter. #2281

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Commits on Sep 17, 2024

  1. Remove the mpileup BAM_CREF_SKIP filter. 

    Mpileup removes alignments using the cigar ref skip operator ("N").
This was originally added in 2011 in samtools/samtools#d1643d6 with
the commit message of "fixed a bug in indel calling related to
unmapped and refskip reads".

Unfortunately I don't know what that bug was, but removing the code
shows it still works (at least for some data!).  We need better
understanding of what's going on and why it was added, so perhaps we
should add a command line option to control this instead?

Fixes samtools#2277
    @jkbonfield
    jkbonfield committed Sep 17, 2024
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