I'm trying to automatically compare BAM files being output by bowtie2 (for a continuous integration system). Currently using `bamUtil diff` which works well, except I'm noticing sometimes 2 lines in the BAM file will have the same name/start position, but represent different reads. For whatever reason, bowtie2 sometimes reverses the order of the lines, so bamUtil's algorithm calls a mismatch. I see several potential solutions to this problem:

1. Get samtools to sort by another dimension in addition to position/name. Pretty much anything should do. Can this be done? I don't see any options in the man page.

2. Use another comparision tool than bamUtil which doesn't have this problem. Honestly a stand-alone program for diffing would be best for me anyway and I'm considering writing one.

3. Find some way to get bowtie2 to be more deterministic in its ordering. Any ideas here? 
Exactly which parts of the alignments do you want to be diffed? If you just care about name/sequence then you can use bamHash. If you want more than that then you'll need a custom solution. There are no options to have samtools sort in a 3rd way (no one has ever needed that).