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Stop treating multiple CIGAR match operations as indels. #1914

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merged 1 commit into from
Apr 27, 2023

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whitwham
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Multiple matching (or sequence (mis)matching)) are treated as containing indels. This can lead to realignment not being called.

Fixes samtools/htslib#1597 in conjunction with samtools/htslib#1607.

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pd3 commented Apr 27, 2023

Thank you

@whitwham whitwham deleted the xme_difference branch September 30, 2024 14:13
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bcftools mpileup behaves differently for cigar M vs =/X
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