Adding a checksum generation method for SAM RG records

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1704 8bce386e-0d6e-43e0-b1ca-608082c0432d
Renaming the RG record checksum utility method

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1705 8bce386e-0d6e-43e0-b1ca-608082c0432d
PFB-395 Adding logging to record progress while writing SAM records to disk

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1707 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added MateCigar to SAMRecord as an optional Attribute ("MC")
- Given a SAMRecord that is part of a pair, the MateCigar attribute (MC) will contain the cigar string for that read's mate iff the mate is mapped
- Added getters (for String and Cigar) to SAMRecord
- Moved utility methods created by Mishali (getClippedAlignmentStart/End...) to SAMRecord and commonified with similar methods for the Read itself
- Added validations to MateCigar (not present when inappropriate, matches the Mate's Cigar String)
- Added unit tests for these validations


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1709 8bce386e-0d6e-43e0-b1ca-608082c0432d
RevertSam now uses instanceMainWithExit instead of instanceMain


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1710 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adding the command line tool RevertOriginalBaseQualitiesAndAddMateCiga

- meant to update a SAM/BAM to include the new Mate Cigar ("MC") optional tag.
- additionally, allows the user to optionally revert the original base qualities ("OQ" optional tag).
- will exit early with an INFO message if the SAM/BAM already has the "MC" tag, and therefore would not
need to be reverted.


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1711 8bce386e-0d6e-43e0-b1ca-608082c0432d
Make sure that the mate CIGAR (MC) does not hang off the end of the reference.  If it does, clip it, the same way we do with the record's CIGAR.


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1712 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add buffering for BAM file writing.  By default this will be 128K.  Buffer size can be controlled via -Dsamjdk.buffer_size=<value>.  Buffer size can be controlled programmatically via SAMFileWriterFactory.setBufferSize() method.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1713 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.109

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1714 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add support for reading, writing and on-the-fly creation of Tabix indices in tribble library.  Now one can request on-the-fly indexing when using VariantContextWriterFactory to create a block-compressed VCF.  In addition, lots of clean-up of the Tribble APIs.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1717 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add buffering when using Snappy.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1718 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix recently-introduced bug in which SAMFileReader.query was not finding unmapped reads that had the coordinate of the mapped mate.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1719 8bce386e-0d6e-43e0-b1ca-608082c0432d
PFB-397 Examples of BCF-related files for testing.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1720 8bce386e-0d6e-43e0-b1ca-608082c0432d
PFB-490 Make sure that SAM, BAM, VCF, BCF reading and writing are buffered where appropriate, and also that things will not fall over when -Dsamjdk.buffer_size=0

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1721 8bce386e-0d6e-43e0-b1ca-608082c0432d
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