BAMtools "Convert, Merge, Randomize" - "Random" option requires sorted input

[jennaj]

Maybe not a true bug, but unexpected input requirements that are not defined on the tool form.

The "Random" function requires that the input BAM/SAM is coordinate sorted. Meaning that SortSam should be run on it. This is true even for Tophat2 BAMs, which are already labeled as being coordinate sorted.

Several tools do not recognize Tophat2 BAMs as being in strict enough coord sort order when required in the input - BAMtools, Picard.

This tool's potential solution: Add comments to the tool form for the option "Random" specifying that the input must be coordinate sorted and to use SortSam first (on ALL?).

Other tool's potential solution: Add comments to use SortSam first, as a default.

Moved from Trello: https://trello.com/c/3nR6TXS0