Changes to add an IterableIterator interface (I thought we had one of these somewhere, but I guess not) and to add a method to IoUtil to read a text file in as an IterableIterator<String> of lines.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1518 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adjusted the LL to probs method to provide a ceiling and floor for probabilities that fit within the range of precision of java.lang.Double

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1519 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changed the construction of output streams to add buffering by default.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1520 8bce386e-0d6e-43e0-b1ca-608082c0432d
Reverting a problematic change.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1521 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added a new program to strip out all per-sample information from a VCF to create a site-only VCF for faster processing when genotypes and other per-sample information is not required.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1522 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'