Merge improvements

For review and consideration.  There are some parts I need to clean up in this, but this is a reasonable second draft now.  I say reasonable because it does as far as I have tested successfully merge BAM files.  It still needs the following cleanups:
1. bam_itr_finish - need to decide what to do with this.
2. Move memset_pattern4 to some utility file?
3. Break trans_tbl_init into multiple functions.
4. Use new header api to do trans_tbl_init instead of regex.
5. Integrate unit tests into make test.
I am having issues building the current revision owing to a kfunc.h related error.  I do not however believe this is related to my changes.