v116-preview

New things:

• Kate has extended liftOver to handle bed+ (needed for ENCODE hg16 to hg17).
• Mark has added support for alignment categories and variables in genbank.conf. The alignment categories are finished (human, for example), ordered (mouse, for example) and lowCoverage (lots of examples).
• Mark added features to pslCDnaFilter (local near best in genome and min non-repeat len) with lots of test cases.
• Angie added src/oneShot/preProcGgfAndy/preProcGgfAndy.c which extracts GC stats from .fa, to be piped to my version of Andy Law's cpg island finding perl script, ggf-andy-cpg-island.pl.
• Heather continues to work on snpMask.
• Bob has a new utility showProcessList.csh.

Bug fixes:

• Jim has fixed a 64 bit bug in jkOwnLib (ffAliHelp.c, ffSeedExtend.c, gfBlatLib.c, supStitch.c).
• Mark has bug fixes in overlapSelect and pslDiff.
• Galt has a bug fix to the ruler in hgTracks, which takes care of the downstream display of other tracks.
• Bob has changes to compareTrackDbs.csh.

Data:

• Hiram is working on monDom2, mm7 and ENCODE.
• Fan is working on miRNA.