XS score in secondary alignments

[fxjonas]

Dear Bowtie2 team,

I am trying to find the all best alignments of true multi mapping read. I hoped this would be possible by using the -k/-a option and only take those were the AS (alignment score) is the same as XS (the best other alignment scores). But there seems to be a problem: While the scores make sense for primary alignments, i.e. AS is higher than XS for unique alignments and equal for true multi mappers, secondary alignments always have AS equal to XS even if the primary alignment has a higher alignment score. So I am wondering if my interpretation of XS and AS is wrong or if there might be a bug in the calculation of the XS score for the secondary alignment?

Thanks for your help, Felix