added some tests to SeekableBufferedStream and fixed insertSizeHistogram.R so that it doesnt get confused by a single quote in the sample name

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1452 8bce386e-0d6e-43e0-b1ca-608082c0432d
oops, forgot to add test file.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1453 8bce386e-0d6e-43e0-b1ca-608082c0432d
Committing this IPR update because IntelliJ appears to prefer its changes.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1454 8bce386e-0d6e-43e0-b1ca-608082c0432d
Bug fix: was calculating average quality of second-reads by using the count for the first-reads (where the second-read count was appropriate).

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1455 8bce386e-0d6e-43e0-b1ca-608082c0432d
Create an interface for Program enum to extend, so that outside developers can add their own Program implementations.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1456 8bce386e-0d6e-43e0-b1ca-608082c0432d
Create an interface for Program enum to extend, so that outside developers can add their own Program implementations to CollectMultipleMetrics.
Fix issues with R scripts when read group library is not populated.
Package R scripts into picard.jar.


git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1457 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed bug in which inability to write barcodes.txt(.gz) file is not detected.
Add unit test for this case.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1458 8bce386e-0d6e-43e0-b1ca-608082c0432d
Amended DefaultingMap entry initialization: hand in the key, too.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1459 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added logging; addressed warnings.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1460 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed possible NPE in log statement.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1461 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.92

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1462 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge changes from upstream 1.92