Adam -
You can store any information you like in a user-defined optional tag.
Alternatively, are the 'N' and 'P' cigar string operators helpful
in your application ? James Bonfield has extensively explored ways
to represent a multiple sequence alignment as a collection of SAM
records in previous postings to this list.
- tom blackwell -
On Wed, 2 Jul 2014, Adam Scott wrote:
> 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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