Fix bug in IntervalTreeMap iteration.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1513 8bce386e-0d6e-43e0-b1ca-608082c0432d
TribbleIndexedFeatureReader reuses SeekableStream for query when possible

-- The previous version of TribbleIndexedFeatureReader would open a new SeekableStream for each call to query().  This behavior is necessary for non-file backed sources (like HTTP) but is amazingly slow when issues a lot of queries against a file.  The new code checks to see if the source path points to a local file, and if so reuses a single SeekableStream for efficient sequential access to a single TribbleIndexedFeatureReader.  Note that the TribbleIndexedFeatureReader isn't thread-safe, nor does it support multiple simultaneous iterators, which brings it more in line with the behavior of SAMFileReaders.
-- As a consequence of this change, clients that weren't calling close() properly on the TribbleIndexedFeatureReader might end up leaking file handles.  Also, it's possible that clients were relying on the previous, unspecified behavior of the TribbleIndexedFeatureReader supporting multiple queries.  Keep an eye out for bugs.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1514 8bce386e-0d6e-43e0-b1ca-608082c0432d
Make running ant test with standard debugger arguments easy

-- Added test.debug property to build.xml, so that running ant test -Dtest.debug=T will cause the tests to be run with -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${test.debug.port} arguments.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1515 8bce386e-0d6e-43e0-b1ca-608082c0432d