e30e926564e223f37e02a3d0ba6b9f04b8d15fce
browser
  Thu Nov 6 09:15:13 2014 +0000
fixing bug where hgLiftOver would not map regions on the gbib. Also adding a progress message so the user has some idea what's going on.
diff --git src/hg/hgConvert/hgConvert.c src/hg/hgConvert/hgConvert.c
index 8ed7fb6..ccaa2a1 100644
--- src/hg/hgConvert/hgConvert.c
+++ src/hg/hgConvert/hgConvert.c
@@ -244,30 +244,31 @@
     chainSubsetOnT(chain, start, end, &subChain, &chainToFree);
     if (subChain != NULL)
 	slAddHead(&chainList, subChain);
     if (chainToFree != NULL)
         chainFree(&chain);
     }
 slSort(&chainList, chainCmpScore);
 return chainList;
 }
 
 static void doConvert(char *fromPos)
 /* Actually do the conversion */
 {
 struct dbDb *fromDb = hDbDb(database), *toDb = hDbDb(cartString(cart, HGLFT_TODB_VAR));
 char *fileName = liftOverChainFile(fromDb->name, toDb->name);
+fileName = hReplaceGbdbMustDownload(fileName);
 char *chrom;
 int start, end;
 int origSize;
 struct chain *chainList, *chain;
 
 cartWebStart(cart, database, "%s %s %s to %s %s", fromDb->organism, fromDb->description,
 	fromPos, toDb->organism, toDb->description);
 if (!hgParseChromRange(database, fromPos, &chrom, &start, &end))
     errAbort("position %s is not in chrom:start-end format", fromPos);
 origSize = end - start;
 
 chainList = chainLoadAndTrimIntersecting(fileName, chrom, start, end);
 if (chainList == NULL)
     printf("Sorry this position couldn't be found in new assembly");
 else