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Mismatched read bases rendered incorrectly #523
Hi - apologies in advance if this stems from a misunderstanding.
The attached screenshot demonstrates what I mean. The popup refers to the bottom-most of the 4 visible reads.
I've checked the underlying BAM and have confirmed that the bases are indeed G/C/C/C/C.
Perhaps this is a bug?
What kind of aligner is being used?
I think the MD is OK - the SAM specification (v1) implies the the MD should show the reference base, not the observed base. In this case, the reference is A, so the MD is fine. The actual observed base on the read is C.
So I guess something else must be going on here?
Thank you very much for providing the data. I think this is actually similar to another recently reported issue
The following additional patch seems to restore functionality for this case
I think it may be wise to go over this code more closely to verify the logic in all cases now!