v131-final

New things:

• Jim has extensive paraFlow edits.
• Hiram added a new util src/utils/mkUsageIndex.sh.
• Angie added a new util src/utils/mkMafFrames.pl: a Perl version of Mark's script to run genePredToMafFrames on a cluster node.
• Mark has a new genbank program to build species lists with counts of cDNAs.
• Andy added a new util src/hg/utils/intervalToBed to convert window masker output to bed.
• Heather has a new util snpPAR.c to generate chrY PAR SNPs from chrX.

Edits:

• Kate has edits to src/hg/makeDb/makeLoChain scripts.
• Kate has chimp specific edits to hgTracks, hgc, hgFind.
• Heather rewrote snpClassAndObserved.c and did snp125 edits from QA review.
• Jim has an hgTracks edit to add a submit button next to reset of custom track.
• Angie has on-going code cleanup (unused variables, cast to int for array index, remove chromEnd index)

Data:

• Angie did rn4 9-way Conservation.
• Galt updated Jackson Lab data for VisiGene.
• Fan added blastz notes to makeHg18.doc.
• Hiram did hg18 coverage track.
• Kate did panTro1 to panTro2 lift.
• Kate did panTro2 reciprocal best.
• Andy updated rebaseRefs in hgFixed and loaded affyHumanExon tables into hg17 and hg18.