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Hi,
I was wondering if there are plans to update winnowmap to include sequence information even if mapping quality is 0 in BAM file? We noticed that when mapping quality is 0 for a read, winnowmap yanks out the sequence information in BAM file. I am attaching a screenshot as an example. It can be seen that the sequence is not present in the last column (where the red dot is).
Thank you for your help in advance!
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Jag
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