Take all the time you need. If you need to bounce ideas off anyone, feel free to reach out.

For what it's worth, there's an ADAM RDD method, "adamSingleReadBuckets", which returns an RDD of "SingleReadBucket" objects. A SingleReadBucket has all the Single/PE reads, primary and secondary alignments for a single read, e.g. a PE mapped read would have two ADAMRecords in the primaryMapped array. Basically, all the information for a single read in a single object. Btw, I'd love any feedback you have on a better name for it if you have it.