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Improve mpileup overlap removal #1751

Merged
merged 2 commits into from
Feb 27, 2024
Merged

Improve mpileup overlap removal #1751

merged 2 commits into from
Feb 27, 2024

Commits on Feb 16, 2024

  1. Improve mpileup overlap removal for deletions 

    The code previously just skipped deletions, meaning templates with a
deletion in one copy and not in the other could still be reported
twice in the mpileup.  Note this depended on what came first due to
the order of iref updates.

The new code moves the two iref updates to after the two
cigar_iref2iseq_next so we're always consistently getting the next
reference base regardless.

We then detect deletions and catch the lagging sequence up, applying
the same Q*=0.8 or Q=0 logic that the mismatching base code does.

It's tricky to know if this has a beneficial impact on variant calling
or not!  If there is debate over whether a deletion exists between the
read-pairs, then it is probably not something we wish to take into
account, however it's currently random which read we select.
Previously we'd have had both deletions and not-deletion present in
the results, over-inflating depth but maybe bringing less confidence
to such deletion calls.  However it is at least consistent with the
stated intention of overlap removal.

One possible further mitigation could be to reduce quality more around
such positions (so not just Q*0.8, and also adjusting the before/after
base too for the deletion read).  That hasn't been done here though.

Fixes samtools/samtools#1992
    @jkbonfield
    jkbonfield committed Feb 16, 2024
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  2. Extend pileup test to include quality values. 

    Without this we cannot test that the overlap removal code is working,
which operates by zeroing quality values.
    @jkbonfield
    jkbonfield committed Feb 16, 2024
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