Release 1.101

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1578 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changed default read name header formatting for fastq records emitted by `IlluminaBasecallsToFastq` to include new values and, in particular, passing-filter flags.  The old read name header formatting is referred to as "Illumina," and the new formatting "Casava 1.8".  This change necessitated adding two new required (by default) arguments: FLOWCELL_BARCODE and MACHINE_NAME.

You may control the formatting emitted by IlluminaBasecallsToFastq with the `READ_NAME_FORMAT` argument.  (For example, pass READ_NAME_FORMAT=ILLUMINA to emulate default functionality prior to this commit.)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1581 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'