5dd57ba4756985d35f8ca72756d963b77934fcf0
angie
  Thu Jun 7 16:08:53 2018 -0700
Expand support for -multiple to BED 3 to 12 (instead of 4 to 6).  refs #18853
Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks.
Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd.

Todo: genePred.  Probably won't bother doing PSL because pslMap should be used for that.  Also removed some very old #ifdef'd code.

diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c
index 0b36f2d..1334c10 100644
--- src/hg/hgLiftOver/hgLiftOver.c
+++ src/hg/hgLiftOver/hgLiftOver.c
@@ -501,31 +501,31 @@
     chmod(unmappedTn.forCgi, 0666);
 
     fromDb = cgiString(HGLFT_FROMDB_VAR);
     toDb = cgiString(HGLFT_TODB_VAR);
     chainFile = liftOverChainFile(fromDb, toDb);
     if (chainFile == NULL)
         errAbort("ERROR: Can't convert from %s to %s: no chain file loaded",
                                 fromDb, toDb);
 
     readLiftOverMap(chainFile, chainHash);
     lft = liftOverSniff(oldTn.forCgi);
     if (lft == bed)
 	ct = liftOverBed(oldTn.forCgi, chainHash, 
 			minMatch, minBlocks, 0, minSizeQ,
 			minChainT, 0,
-			fudgeThick, mapped, unmapped, multiple, NULL, &errCt);
+                        fudgeThick, mapped, unmapped, multiple, FALSE, NULL, &errCt);
     else if (lft == positions)
 	ct = liftOverPositions(oldTn.forCgi, chainHash, 
 			minMatch, minBlocks, 0, minSizeQ,
 			minChainT, 0,
 			fudgeThick, mapped, unmapped, multiple, NULL, &errCt);
     if (ct == -1)
         /* programming error */
         errAbort("ERROR: Unsupported data format.\n");
 
     webNewSection("Results");
     if (ct > 0)
         {
         /* some records succesfully converted */
         cgiParagraph("");
         printf("Successfully converted %d record", ct);