v138-preview

Code changes:

• Ongoing work on hgAutomate (Angie)
• Added utility to print SQL commands for adding new genome DB table to QA pushQ (Angie)
• Fixed some bugs in chainStitchID reallocation code (Angie)
• Updated protein makefile, resolved many -Wall warnings (Angie)
• Modified hgTables/bedList.c to replace space w/"-" in bed->name (Angie)
• Added mod to hgTracks to allow user to reorder tracks (Robert)
• Added -noMask option to twoBitToFa (Robert)
• Added mods to support GAD track processing (Fan)
• Added mods to hide Swiss-Prot entries in Human Mutation tracks by default (Belinda)
• Added support for dbRIP track (Hiram)
• Modified hgLoadBed to use -ignoreEmpty to allow empty custom tracks (Hiram)
• Modified liftOverChain.c to avoid duplicate entries in liftOverChain table (Kate)
• Added utility to drop split tables from DB (Kate)
• Added QA tool for getting stats on a user (Bob)
• Added support for enum and set columns to autoSql (MarkD)
• Improved pslMap error msg when sequence sizes don't match (MarkD)
• Fixed problem w/mafFlipStrand getting start wrong (MarkD)

Data changes:

• Added galGal3 bacEndPairs (Angie)
• Added hg17 genomicSuperDups (Angie)
• Added GAD track (Fan)
• Added affyZonWildType array data track (Rachel)
• Added affyZebrafish track, added human orthologs table (Rachel)
• Reloaded hg17 genscanPep and geneidPep tables (Rachel)
• Added mm8 ensPep table (Rachel)
• Added dbRIP track (Hiram)
• panTro2 updates: finished danRer4 alignments, redid hg17 alignments, updated chrY agp (Kate)