svn ignore intellij output directories.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1529 8bce386e-0d6e-43e0-b1ca-608082c0432d
Force compiler to use Java 6 bootclasspath even if JAVA_HOME is Java 7.  In order to do this, either the environment variable JAVA6_HOME must point to Java 6 JAVA_HOME, or -Djava6.home=<path> must be put on the ant command line.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1530 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changed DelimitedTextFileWithHeaderParser to DelimitedTextFileWithHeaderIterator, which involved changing it from being an Iterable to an Iterator

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1531 8bce386e-0d6e-43e0-b1ca-608082c0432d
Tied to #1531, managed to not include these files

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1532 8bce386e-0d6e-43e0-b1ca-608082c0432d
When generating a site-only VCF, do not regenerate the alleles based on the subsetted genotypes.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1533 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'