More custom words.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1516 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed isSimpleInsertion() and isSimpleDeletion() in the VariantContext, per Tim's long-ago request.
They now both check that the first base of ref is equal to the first base of alt.
Added isSimpleIndel() too.
Added unit test to cover the case of complex substitutions (the motivation for this report).



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1517 8bce386e-0d6e-43e0-b1ca-608082c0432d
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
Added DelimitedTextFileWithHeaderParser, an attempt to transition toward a replacement for TabbedTextFileWithHeaderParser with more flexible delimiter possibilities. Currently nearly a line for line copy of TabbedTextFileWithHeaderParser although the intention is to transition the latter to be a wrapper around the former.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1523 8bce386e-0d6e-43e0-b1ca-608082c0432d
Removing extraneous directory.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1524 8bce386e-0d6e-43e0-b1ca-608082c0432d