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marbl / Winnowmap

Long read / genome alignment software
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Sequence information not present in BAM file when mapping quality is 0 for a read #47

Open jagadhesh89 opened 2 months ago

jagadhesh89 commented 2 months ago

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).

0 mapping quality

Thank you for your help in advance!

-- Jag

cjain7 commented 2 months ago

We had directly borrowed input / output formatting logic from minimap2 without any modification. I see some useful information here

https://github.com/lh3/minimap2/issues/458 https://github.com/lh3/minimap2/issues/526

It looks like people recommend using -Y input parameter.