Meaningful MAPQ values would be excellent.

[JohnUrban]

Hi all,

I am trying out Magic-BLAST for mapping short-reads, and may want to test it in various pipelines.

I noticed, however, that the MAPQ field in the SAM output is either 0 or 255.

At first I thought that might be a classification of "multiread" vs "unique", however I then noticed it was just "unmapped" vs "mapped".

Are there plans to add more meaningful MAPQ values in the future? By "meaningful" I mean any of the following:

• a non-binary distribution of possible values (e.g. ranging from 0-40 or 0-60).
• values that correlate with the original MAPQ meaning ... something like -10*log10( probability the read was mapped to the wrong spot )

In terms of a feature request, I think more meaningful MAPQ values would make Magic-BLAST more straightforward to adapt into my own pipelines, thinking, and approaches. Perhaps for others as well.

Let me know if I am missing something.

What exactly was the intended use case for Magic-BLAST? Was it meant to potentially replace older progams in pipelines (e.g. bowtie2, BWA, etc)?

Best,

John