Add final

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1364 8bce386e-0d6e-43e0-b1ca-608082c0432d
Trim /1 and /2 suffixes when merging from alignments for first and second end separately.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1365 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add test (currently disabled) for SamLocusIterator with emitUncoveredLoci == true, because there is a bug.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1366 8bce386e-0d6e-43e0-b1ca-608082c0432d
git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1367 8bce386e-0d6e-43e0-b1ca-608082c0432d
git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1368 8bce386e-0d6e-43e0-b1ca-608082c0432d
git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1369 8bce386e-0d6e-43e0-b1ca-608082c0432d
Compute 5' position properly regardless of sign of inferred insert size.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1370 8bce386e-0d6e-43e0-b1ca-608082c0432d
RRBS QC Metrics

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1371 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add two new PrimaryAlignmentStrategies BestEndMapq and MostDistant

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1372 8bce386e-0d6e-43e0-b1ca-608082c0432d
Revert previous change to getPairOrientation.
Improve unit tests.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1373 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.87

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1374 8bce386e-0d6e-43e0-b1ca-608082c0432d
Switch to svn+ssh url

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1381 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge changes from svn 1.87