v114-preview

On-going work:

• Hiram is continuing to work on randomPlacement.c.
• Galt is continuing to work on visiGene.
• Rachel is continuing to work on danRer3.

New things:

• Fan has 2 new utilities in src/hg/protein: KGcgap.sh and KGpath.sh.
• Hiram added a -lift option to wigEncode.
• Mark added filter options to pslCheck.
• Donna moved the "Convert" link to point to hgLiftOver.
• Brian changed hgc to predicted proteins to show stop codons as XXX rather than not showing anything.

Bug fixes:

• Hiram changed hgTracks.c to show the refresh button even if no track controls are visible (this was on the ENCODE wish list).
• Angie changed hgMaf.c to sort results in mafLoadInRegion, because hRangeQuery may return items out-of-order when bin is used in the query (she sent a separate email on this).
• Fan fixed a bug in gfOut.c that caused negative target coordinates when the query is a protein sequence and database is DNA.

Data:

• Rachel loaded a new GO database.
• Rachel reloaded the cgap* tables.
• Fan added sections to makeProteins050415.doc regarding spVariant and proteome.
• Hiram has ENCODE track improvements.
• Jen, Brian and Katie Pollard have trackDb edits.