Remove 'bam2adam' in favor of 'transform'

This removes the `bam2adam` command since it can be replaced with a no-op invocation of `transform`.

Upsides:

1. Preserves sort ordering.
2. Seems to more cleverly choose the number of partitions, obviating the need for the `-num_threads` option previously used to set the partitioning level.
3. Supports distributed operation and reading from HDFS, instead of local operation and only `file://` URIs.

Downside: doesn't (yet) support changing the SAMtools validation level.