v130-final

New things:

• Jim has extensive edits to paraFlow.
• Mark added handling of haplotype pseudochroms to pslCDnaFilter.
• Kate added utils/agpToLift.
• Mark added -strand test for -selectRange to overlapSelect.
• Mark added sanityErrSum; summary stats for gbSanity.
• Galt added a new function sqlSaveQuery() to jksql.c.
• Andy added a new function slNameFindIx() to common.c.
• Heather rewrote apacheMonitor in C.

Edits:

• Kate changed findRefGenes() to use the new genePredReader, which will handle refGene tables with a bin column.
• Angie has on-going code cleanup.
• Robert Baertsch has edits to pslPseudo.c.
• Andy has edits to expClick.c for the Affy Exon Array track.

Bug fixes:

• Angie had a bug fix to hgTables: "Bumped up the dispatch order of doMainPage and doSchema, so that links in will do the right thing even if some hgta_do* variables got stuck in the cart during previous errors about conflicting settings, e.g. all fields and intersection."
• Galt fixed a qaPushQ bug.

Data:

• Todd Lowe added new archae data.
• Hiram did self blastz for mm8.
• Hiram is working on chains/nets for monDom4.
• Hiram is working on protein alignments for hg18.
• Fan did hg18 to hg17 liftOver.
• Kate fixed panTro2 chr9.
• Rachel finished danRer3 RH map.
• Angie is working on rheMac2 and rn4.
• Mark added the NSCAN track for canFam1.