Investigate and improve the pipeline's read-merging behavior

[harmonbhasin]

Jeff did some digging around and found some weird behavior between bbmerge and bowtie2 where paired reads that we'd expect to be merged aren't always merged and vice versa. It would be good to know how often this happens, and see if we can prevent this behavior from happening by changing parameters in one or both of the softwares.

[willbradshaw]

Further investigation suggests that we do have a genuine issue here, where about 5-10% of reads are being incorrectly merged by BBMerge in a way that other approaches to merging can handle better. While this isn't a terrible failure rate, we should still investigate and see if we can improve the situation.