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

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1449 8bce386e-0d6e-43e0-b1ca-608082c0432d
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: http://svn.code.sf.net/p/picard/code/trunk@1452 8bce386e-0d6e-43e0-b1ca-608082c0432d
oops, forgot to add test file.

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

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

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

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1462 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix header of test VCF so that it passes validation


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1465 8bce386e-0d6e-43e0-b1ca-608082c0432d
Set javac.target to 1.6

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1466 8bce386e-0d6e-43e0-b1ca-608082c0432d
Speed up validation for headers with many read group records.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1467 8bce386e-0d6e-43e0-b1ca-608082c0432d
Support both gzipped and normal BCL files. This now uses a BufferedReader instead of a memory map backed iterator

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1468 8bce386e-0d6e-43e0-b1ca-608082c0432d