Tabix indices are block-compressed files

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1763 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add BC tag

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1766 8bce386e-0d6e-43e0-b1ca-608082c0432d
Re-order enum values for known IlluminaAdapterPairs so most permissive one is at the end.  This is important for unit testing where all of them are tried.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1767 8bce386e-0d6e-43e0-b1ca-608082c0432d
Speed up adapter-finding code, which is used in IlluminaBasecallsToSam, IlluminaBasecallsToFastq, and MarkIlluminaAdapters.  By default, adapter sequences will be truncated at 30 characters, and any adapter pairs that become duplicates as a result are folded together.  After 100 adapters have been identified in reads, the list of adapter candidates is pruned down to the one adapter pair that was most frequent among the 100 reads with adapter sequence found.  In small tests, this has reduced IlluminaBasecallsToSam execution time by about 40%.  Moreover, since in most cases an Illumina lane uses only one adapter pair, pruning the list down to one pair reduces the chance that a read will be incorrectly marked with an adapter pair that was not used in the lane.  Note that for IlluminaBasecallsToSam and IlluminaBasecallsToFastq, there is no control over the configuration of this functionality.  However, MarkIlluminaAdapters has new command-line options that control all of the above behavior.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1768 8bce386e-0d6e-43e0-b1ca-608082c0432d
Work around erroneous Java 6 compilation error


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1769 8bce386e-0d6e-43e0-b1ca-608082c0432d
release script no longer copies /picard/trunk to /picard/branches


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1770 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add .gzip to BLOCK_COMPRESSED_EXTENSIONS

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1771 8bce386e-0d6e-43e0-b1ca-608082c0432d
Refactored the action into the ENUM (from a switch)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1772 8bce386e-0d6e-43e0-b1ca-608082c0432d
Replace .idx and .tbi with appropriate constants

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1773 8bce386e-0d6e-43e0-b1ca-608082c0432d
Implement `Closeable` to facilitate try-with-resources in Java 7+ projects that depend on picard.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1774 8bce386e-0d6e-43e0-b1ca-608082c0432d
Create lane directories for symlinks if they don't exist.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1885 8bce386e-0d6e-43e0-b1ca-608082c0432d
Reassign the file util when checking symlinks since the original one caches file locations.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1889 8bce386e-0d6e-43e0-b1ca-608082c0432d
Revert modified function arguments.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1890 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merged nh_mate_cigar_refactoring r1775:r1889 into trunk

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1891 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added support for VCFv4.2 Version tags in header fields.



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1894 8bce386e-0d6e-43e0-b1ca-608082c0432d