Change to SeekableBufferedStream to implement skip() directly by either positioning ahead in the buffer or seek()ing instead of relying on InputStream.skip() which reads through the entire skip.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1445 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed a parameter name to be more clear.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1446 8bce386e-0d6e-43e0-b1ca-608082c0432d
Bug fix when converting (double) GLs into integer PLs: code was saturating at Short.MAX_VALUE = 32767. This is an issue with large events or when very high depth where PLs will be incorrect and saturate to this value.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1447 8bce386e-0d6e-43e0-b1ca-608082c0432d
Producing the right result if INTERLEAVE=false and SECOND_END_FASTQ is not null.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1448 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.91

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1449 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge upstream version 1.91