Exception if template alignment records are out of order

AlignmentFilter should take records (for same primary data) from
multiple BAM files - if template groups f reocrds or out of order
compared with the first file, or missing form the first file then
an exception should be thrown.
Fix unchecked conversion javac lint warning for ArrayList
Merge pull request #2 from dkj/devel

Explode if templates are out of order