Modify SAMFileReader.streamLooksLikeBam to accept URL

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1553 8bce386e-0d6e-43e0-b1ca-608082c0432d
Bug fix: if SEQUENCE_DICTIONARY is null, NullPointerException is necessarily thrown.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1554 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added utility to IoUtil.
* #slurp accepts File.
* New method #slurpLines to return a list of lines in a file.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1555 8bce386e-0d6e-43e0-b1ca-608082c0432d
Compile fix: doesn't like special characters.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1556 8bce386e-0d6e-43e0-b1ca-608082c0432d
eliminate Scanner class usage

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1557 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.99

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1558 8bce386e-0d6e-43e0-b1ca-608082c0432d