Made method 'doWork' public in RevertOriginalBaseQualitiesAndAddMateCigar so that it can be accessed by another tool more easily.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1722 8bce386e-0d6e-43e0-b1ca-608082c0432d
Revert changes in `SamPairUtil#setMateInfo()` which introduced setting of the mate cigar string.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1723 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed a bug in how the validation of cigar strings was adapted to handle mate cigar strings.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1724 8bce386e-0d6e-43e0-b1ca-608082c0432d
Try loading index, even if one not required

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1725 8bce386e-0d6e-43e0-b1ca-608082c0432d
Small change to allow MakeSitesOnlyVcf retain genotypes for one or more samples.  In this mode all annotations are retained from the full file as if making a sites only file - not recomputed from the retained samples.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1726 8bce386e-0d6e-43e0-b1ca-608082c0432d
Address bugs with `ExtractIlluminaBarcodes`.
- Resolve hang that occured when `ExtractIlluminaBarcodes` encounters an exception in `main` before it finishes submitting all runnables to thread pool.
- Resolve state exception that occurs processing gzipped BCLs with buffered inputs.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1727 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add support for handling phasing metrics from the TileMetricsOut.bin file

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1728 8bce386e-0d6e-43e0-b1ca-608082c0432d
That was weird, there were some hidden (and unwanted) unicode chars in the comments

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1729 8bce386e-0d6e-43e0-b1ca-608082c0432d
Lazy load index file

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1730 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adding ATTRIBUTES_TO_REMOVE option to MerbeBamAlignment, so we can
remove attributes from the incoming alignments.  This option will
override ATTRIBUTES_TO_RETAIN when the conflict.


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1731 8bce386e-0d6e-43e0-b1ca-608082c0432d
Gracefully handle scenario in `MergeBamAlignment` in which a record is mapped completely off the end of the reference by making it unmapped.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1732 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix critical typo in query method

hasIndex -> !hasIndex

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1733 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added SamFileTester to facilitate creation and testing of "on the fly" SAM files. (examples included in CleanSamTest and MarkDuplicatesTest)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1734 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added the ability to pass an expected quality format to QualityEncodingDetector

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1735 8bce386e-0d6e-43e0-b1ca-608082c0432d
Bug fix: `AsynchronousLineReader` fails to propagate worker thread errors that aren't `Exception`s.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1736 8bce386e-0d6e-43e0-b1ca-608082c0432d
- moving SamPairUtil from net.sf.picard.sam to net.sf.samtools since SAMRecordSetBuilder depends on it
- SamFileValidator now has a method with no expected base quality format



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1737 8bce386e-0d6e-43e0-b1ca-608082c0432d
- default quality format now enabled in ValidateSamFile


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1738 8bce386e-0d6e-43e0-b1ca-608082c0432d
- when generating synthetic mate pairs, if both ends had the same start, position, and strand, then only one of the two would be added
- input files were being created in the source code directories, now being created in the temporary (output) directory


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1739 8bce386e-0d6e-43e0-b1ca-608082c0432d
moving SamPairUtilTest from net.sf.picard.sam to net.sf.samtools, to accompany the previous move of SamPairUtil


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1740 8bce386e-0d6e-43e0-b1ca-608082c0432d
Non-ascii character introduced into a command line option documentation string.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1741 8bce386e-0d6e-43e0-b1ca-608082c0432d