Illumina bug workaround: Parser for TileMetricsOutput.bin ignore will discard duplicate entries.  (Previously, if duplicate entries were found, the parser could get confused and couldn't collate the tile data properly.)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1481 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.94

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1482 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added logging for VcfFormatConverter.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1485 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'