New VariantContextWriterBuilder class and tests

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1896 8bce386e-0d6e-43e0-b1ca-608082c0432d
setting ADD_MATE_CIGAR to default to true in FixMateInformation and MergeBamAlignment.


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1899 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.111

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1900 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add ability to remap sample names for single-sample vcfs to the vcf codec

By calling setRemappedSampleName() on an instance of a vcf codec, you instruct
it to replace the existing sample name in the vcf header with a new value. Attempting
to use this feature with multi-sample or sites-only vcfs throws an error.



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1902 8bce386e-0d6e-43e0-b1ca-608082c0432d