#102 Ability to modify -a behavior keeping only best alignments

[Andras]

Hi Ben & all,

I know Bowtie is not designed with -a mode in mind, but if it's there, I believe it might as well support all-best mapping, that is, not reporting suboptimal alignments.

Of course I can easily emulate this behavior by dropping every row in the SAM file for which AS != XS (at least in a single-end scenario) but it's extremely wasteful, as it involves not only tons of I/O but lots of wasted CPU cycles during mapping, calculating alignments of reads that are known to be suboptimal right in the earliest seeding/backtracking steps.

I'm thinking of something like --distance-range in RazerS3, although a simple --best-only would be perfectly good as well. Do you think it's a reasonable feature request for Bowtie2?