3a820099ba5196fde3ae3b1a1489f78f02221568
angie
  Fri Oct 12 09:42:02 2012 -0700
Fixing liftOver of bedPlus, copy-paste-forget-edit bug introduced inb224dbbd -- important arguments of liftOverBedPlus were discarded,
like bedPlus(!), hasBin and tabSep.

diff --git src/hg/lib/liftOver.c src/hg/lib/liftOver.c
index 7e20e1c..95e2893 100644
--- src/hg/lib/liftOver.c
+++ src/hg/lib/liftOver.c
@@ -1182,31 +1182,31 @@
 lineFileClose(&lf);
 return ct;
 }
 
 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 N+ file.
  * Return the number of records successfully converted */
 {
 return liftOverBedPlusEnds(fileName, chainHash, minMatch, minBlocks,
                         minSizeT, minSizeQ, minChainT, minChainQ,
                         fudgeThick, f, unmapped, multiple, chainTable,
-			    0, FALSE, FALSE, 0, errCt);
+			bedPlus, hasBin, tabSep, 0, errCt);
 }
 
 int liftOverBed(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)
 /* Open up file, decide what type of bed it is, and lift it. 
  * Return the number of records successfully converted */
 {
 return liftOverBedPlus(fileName, chainHash, minMatch, minBlocks,
                         minSizeT, minSizeQ, minChainT, minChainQ,
                         fudgeThick, f, unmapped, multiple, chainTable,
                         0, FALSE, FALSE, errCt);