Support for the 0x800 supplementary alignment flag within Picard. Tools which previously only processed primary and ignored secondary alignments will now ignore secondary and supplementary. MergeBamAlignment will pass supplementary alignments along in the output BAM.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1501 8bce386e-0d6e-43e0-b1ca-608082c0432d
Have test point to proper output path

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1502 8bce386e-0d6e-43e0-b1ca-608082c0432d
Rolling back a few changes from previous commit; refactor to address test issues forthcoming to reintroduce these changes.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1503 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'