Sort order is not strictly preserved

[tantrev]

Not sure if this is a bowtie issue or bison, but the aligned reads from bison do not seem to be properly sorted by read ID. For example, here are 20 read IDs from a file I've been aligning using bison:

SRR892990.1.1
SRR892990.2.1
SRR892990.3.1
SRR892990.4.1
SRR892990.4.2
SRR892990.5.1
SRR892990.5.2
SRR892990.1.2
SRR892990.2.2
SRR892990.3.2
SRR892990.6.1
SRR892990.6.2
SRR892990.7.1
SRR892990.7.2
SRR892990.8.1
SRR892990.9.1
SRR892990.10.1
SRR892990.11.1
SRR892990.11.2
SRR892990.12.1

Some programs like Samblaster, expect the aligned reads to be sorted so that "SRR892990.1.2" is located immediately after "SRR892990.1.1".