b224dbbd105b929a99841a7dd11526cc0b1a5422
aamp
  Fri Sep 14 11:20:42 2012 -0700
Changed liftOver to allow big-sized items by just lifting the ends.  Needed library changes as well.
diff --git src/hg/inc/liftOver.h src/hg/inc/liftOver.h
index f8b48a6..f501281 100644
--- src/hg/inc/liftOver.h
+++ src/hg/inc/liftOver.h
@@ -43,30 +43,38 @@
                         int minSizeT, int minSizeQ,
                         int minChainT, int minChainQ,
                         bool fudgeThick, FILE *f, FILE *unmapped, 
                         bool multiple, char *chainTable, int *errCt);
 /* Open up file, decide what type of bed it is, and lift it. 
  * Return the number of records successfully converted */
 
 int liftOverBedPlus(char *fileName, struct hash *chainHash, double minMatch,  
                     double minBlocks, int minSizeT, int minSizeQ, int minChainT,
                     int minChainQ, bool fudgeThick, FILE *f, FILE *unmapped, 
                     bool multiple, char *chainTable, int bedPlus, bool hasBin, 
                     bool tabSep, int *errCt);
 /* Lift bed with N+ (where n=bedPlus param) format.
  * Return the number of records successfully converted */
 
+int liftOverBedPlusEnds(char *fileName, struct hash *chainHash, double minMatch,  
+                    double minBlocks, int minSizeT, int minSizeQ, int minChainT,
+                    int minChainQ, bool fudgeThick, FILE *f, FILE *unmapped, 
+                    bool multiple, char *chainTable, int bedPlus, bool hasBin, 
+			bool tabSep, int ends, int *errCt);
+/* Lift bed N+ file.
+ * Return the number of records successfully converted */
+
 int liftOverPositions(char *fileName, struct hash *chainHash, 
                       double minMatch,  double minBlocks, 
                       int minSizeT, int minSizeQ,
                       int minChainT, int minChainQ,
                       bool fudgeThick, FILE *f, FILE *unmapped, 
 		      bool multiple, char *chainTable, int *errCt);
 /* Create bed file from positions (chrom:start-end) and lift.
  * Return the number of records successfully converted */
 
 int liftOverBedOrPositions(char *fileName, struct hash *chainHash, 
                         double minMatch,  double minBlocks, 
                         int minSizeT, int minSizeQ,
                         int minChainT, int minChainQ,
 		        bool fudgeThick, FILE *mapped, FILE *unmapped, 
 			   bool multiple, char *chainTable, int *errCt);