Allow BAM/SAM files as input to the 'transform' command.

This commit adds Hadoop-BAM back to ADAM and allows users to use BAM/SAM files as
input to the transform command.

Running e.g.

$ adam transform foo.bam foo.adam

will execute a simple file transform from BAM to ADAM formats.

Running e.g.

$ adam tranform -mark_duplicate_reads foo.bam foo.adam

will load the BAM file, mark duplicates and then save to the ADAM format.