Added slurp utility method.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1505 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added funcitonality to .bcl-reading command line programs to better handle qualities less than 2 via BclQualityEvaluationStrategy.  When an application encounters such a quality score, it used to throw an exception immediately; now, it will convert write a quality 1 to the underlying file (bam, fastq, etc.), and at the end of reading the BCLs, it may or may not throw an exception depending on the strictness of the BclQualityEvaluationStrategy.  It will always log a warning message if a quality is encountered, regardless of whether or not an exception is thrown.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1506 8bce386e-0d6e-43e0-b1ca-608082c0432d
Configure Picard-public so that (1) IntelliJ and ant compile to different places and (2) IntelliJ ignores all of the ant compile locations (so that, for example, it does see all the ant .class files and think they are part of the source).  This should prevent ant builds from having an effect on how IntelliJ operates.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1507 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'