Samtools does not seem to care for insertion-deletion events co-occurring,
for example, 9M5I4D62M, will cause error when doing SAM to BAM conversions.
This issue was identified previously here
<https://sourceforge.net/p/samtools/mailman/message/25522310/>. The
recommendation then was to use other tools, but I would like to know if
there might be a way to update samtools to account for this issue. It is
important for my application to retain the true CIGAR string instead of
taking the net indel result (9M5I4D62M --> 9M1I62M).
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