Handle null name in IntervalListComparator.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1470 8bce386e-0d6e-43e0-b1ca-608082c0432d
Change storage of tile # from byte to short in order to handle tile numbers > 127.
Emit warning once for MarkDuplicates and EstimateLibrarySize if the user-supplied READ_NAME_REGEX does not match a read name.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1471 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add limited validation of match against default READ_NAME_REGEX.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1472 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'