bwa aln -m maximum entries in the queue not documented in manual

[marykthompson]

What is the meaning of the -m option for bwa aln? It is only described at the command line as 'maximum entries in the queue', but I cannot find any description of it in the BWA manual to explain what it does. How would changing this parameter from the default affect my results? I want to be sure to find all matches between my query and the genome up to a given edit distance.

Specifically, let's say that I want to find all matches to my query with up to 2 mismatches in a very large genome. How do I know if I have set this -m option high enough to guarantee that all of those matches are found? If I am finding results with 3 mismatches output at a given -m value, does that mean that all alignments with up to 2 mismatches have definitely been found?

I found this question on the mailing list, but without an answer, so I decided to try here. It might be nice to add this to the manual in the future. Thanks.