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/inc/liftOverChain.h src/hg/inc/liftOverChain.h
index a0eecd6..7b927b2 100644
--- src/hg/inc/liftOverChain.h
+++ src/hg/inc/liftOverChain.h
@@ -7,31 +7,31 @@
 
 #ifndef JKSQL_H
 #include "jksql.h"
 #endif
 
 #define LIFTOVERCHAIN_NUM_COLS 9
 
 struct liftOverChain
 /* Chain file for lifting annotations between assemblies */
     {
     struct liftOverChain *next;  /* Next in singly linked list. */
     char *fromDb;	/* Short name of 'from' database.  'hg15' or the like */
     char *toDb;	/* Short name of 'to' database.  'hg16' or the like */
     char *path;	/* Path to chain file */
     float minMatch;	/* Minimum ratio of bases that must remap. */
-    unsigned minSizeT;	/* Minimum chain size in target. */
+    unsigned minChainT;	/* Minimum chain size in target. */
     unsigned minSizeQ;	/* Minimum chain size in query. */
     char multiple[2];	/* Use -multiple by default. */
     float minBlocks;	/* Min ratio of alignment blocks/exons that must map. */
     char fudgeThick[2];	/* If thickStart/thickEnd is not mapped, use the closest mapped base. */
     };
 
 void liftOverChainStaticLoad(char **row, struct liftOverChain *ret);
 /* Load a row from liftOverChain table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct liftOverChain *liftOverChainLoad(char **row);
 /* Load a liftOverChain from row fetched with select * from liftOverChain
  * from database.  Dispose of this with liftOverChainFree(). */
 
 struct liftOverChain *liftOverChainLoadAll(char *fileName);