bigdatagenomics/adam — pull request #54 by jey (2014-01-15 21:02:44+00:00)
Title: Remove 'bam2adam' in favor of 'transform'

This removes the `bam2adam` command since it can be replaced with a no-op invocation of `transform`.

Bonus: preserves sort ordering and (seems to) more cleverly choose the number of partitions, obviating the need for the `-num_threads` option previously used to set the partitioning level.

Downside: doesn't (yet) support changing the SAMtools validation level.