Output not read-name sorted

[brendanofallon]

Looks like in some circumstances the output is not sorted by read name. Technically speaking I think this is fine (the output is still valid .sam as far as I can tell), but read-name sorting is required for some downstream tools, like PCR-duplicate marking methods.
Not really sure if this is a bug or just a nice-to-have feature request, but I think it would smooth adoption if output was more similar to other aligners.

[agudys]

Hi! We'll try to add this feature as soon as possible.

[agudys]

We are currently working on a switch which preserves order of sequences from input FASTQ files (it will affect time and memory requirements, thus we want to provide it as an optional mode).