Update old function-names to match calls.
Record BWA CLI parameters in PG tags.
Add IsDict test.
Add ability to ignore missing input files.

This works for input lanes (untrimmed) and BAMs, and requires that
the mapping/cleanup has already been carried out. This allows the
pipeline to be run, even if (for example) the server housing the
read-data is down.

Also fixed a couple of bugs introduced by the recent changes.