9c92205b58d6b9319f67782c79df1afc154dacd0
galt
  Thu Mar 31 00:13:38 2011 -0700
fixing hgLiftOver: grouping and slightly re-ordering options; adding a new section to show what parameters were actually used to display the results, since code currently resets most options to the values in the chain liftOverChains record; also renamed minSizeT to minChainT since that is what it really is, everywhere except liftOverChain.as and the actual db tables and liftOverChain.sql
diff --git src/hg/lib/liftOverChain.as src/hg/lib/liftOverChain.as
index 9fa9d62..4473f8c 100644
--- src/hg/lib/liftOverChain.as
+++ src/hg/lib/liftOverChain.as
@@ -1,13 +1,13 @@
 table liftOverChain
 "Chain file for lifting annotations between assemblies"
     (
     string  fromDb;	"Short name of 'from' database.  'hg15' or the like"
     string  toDb;	"Short name of 'to' database.  'hg16' or the like"
     lstring path;	"Path to chain file"
     float minMatch;     "Minimum ratio of bases that must remap."
-    uint minSizeT;      "Minimum chain size in target."
+    uint minSizeT;      "Minimum chain size in target. Should be renamed to minChainT"  
     uint minSizeQ;      "Minimum chain size in query."
     char[1] multiple;   "Use -multiple by default."
     float minBlocks;    "Min ratio of alignment blocks/exons that must map."
     char[1] fudgeThick; "If thickStart/thickEnd is not mapped, use the closest mapped base."
     )