src/hg/makeDb/trackDb/README 1.77

Index: src/hg/makeDb/trackDb/README
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/README,v
retrieving revision 1.76
retrieving revision 1.77
diff -b -B -U 4 -r1.76 -r1.77
--- src/hg/makeDb/trackDb/README	2 Jun 2009 19:14:49 -0000	1.76
+++ src/hg/makeDb/trackDb/README	12 Jun 2009 23:35:24 -0000	1.77
@@ -456,8 +456,22 @@
       than showCdsMaxZoom  to make this useful.
     o nextItemButton off - For tracks that have next-item buttons that
       shouldn't, turn the buttons off until whatever else is fixed.
 
+Specific, optional settings used only by snp125, snp126, and so on:
+    o chimpMacaqueOrthoTable table - table contains orthologous
+      alleles from the reference assemblies of chimp and macaque.
+    o chimpOrangMacOrthoTable table - same as above, plus orangutan.
+    o {chimpDb,orangDb,macaqueDb} db - database used for the
+      respective species' alignments when generating the OrthoTable.
+    o codingAnnotations table1,table2,... - each table describes
+      changes in a particular gene set's coding sequence caused by SNPs.
+    o codingAnnoLabel_<tableN> - proper name of geneSet for tableN in 
+      codingAnnotations' table list
+    o hapmapPhase {II,III} - older tracks used HapMap Phase II data
+      collected in a table "hapmapAllelesSummary".  Newer tracks use
+      hapmapSnps* tables directly.
+
 
 Note: We have a restriction on table names: Track names (i.e. table
 names, but omitting any chr*_ prefix) should not contain any
 underscores.  We use underscores in track table names to find sequence