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Maybe fix #2599 - #2600

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dpryan79 wants to merge 1 commit into
samtools:developfrom
dpryan79:maybe_fix_2599
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dpryan79 wants to merge 1 commit into
samtools:developfrom
dpryan79:maybe_fix_2599

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@dpryan79

@dpryan79 dpryan79 commented Oct 6, 2026 •

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Given a ./. call that's a deletion, treat it the same as a REF call and mask the entire deleted stretch. Fixes #2599, but someone who knows more about the code should really check whether this makes sense at all :)

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Mismatch between ref and fasta due to incorrect modification of rec1_t

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