Sequence information not present in BAM file when mapping quality is 0 for a read

[jagadhesh89]

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!

--
Jag

[cjain7]

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

lh3/minimap2#458
lh3/minimap2#526

It looks like people recommend using -Y input parameter.