v117-final

New stuff:

• Mark added a new option to faTrans.c to get cds from upper case.
• Mark added a new feature to gbAlignSetup to handle unplaced chroms even if no gap.
• Brian added a routine to twoBit.c to output a bed file with N locations.
• Jim added a new feature to hgVisiGene.
• Hiram added a zeroBed option to randomPlacement.c.
• Angie added an -hgConf option to buildTableDescriptions.pl.

Bug fixes:

• Brian fixed a bug in cds.c where missing CDS caused errAbort.
• Kate made cosmetic changes to hgLiftOver.c for failure cases.

Data:

• Hiram has checked in makeMm7.doc. (Some sections still to-be-done).
• Galt has checked in makeBosTau2.doc.
• Chuck added to makeHg17.doc for 3 tracks: exonWalk, altGraphX, affyTxnPhase2.
• Brian added human proteins for dm2 and fr1.
• Daryl added the regPotential5x track to hg17.
• Fan added the Gene Network track to mm6.