bfcfffa0ad0401f5264bb656e569a78a12847e12
aamp
  Tue Feb 28 15:59:13 2012 -0800
changed hgLiftOver to only output message out multiple option not being suppported for the positions format ONLY if the input is positions format and if the multiple option is checked
diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c
index 28c9292..cd2efe2 100644
--- src/hg/hgLiftOver/hgLiftOver.c
+++ src/hg/hgLiftOver/hgLiftOver.c
@@ -467,57 +467,64 @@
 if (lastChain && thisChain && sameString(lastChain, thisChain))
     keepSettings = TRUE;
 
 webMain(choice, multiple, keepSettings, minSizeQ, minChainT, minBlocks, minMatch, fudgeThick);
 liftOverChainFreeList(&chainList);
 
 if (!refreshOnly && userData != NULL && userData[0] != '\0')
     {
     struct hash *chainHash = newHash(0);
     char *chainFile;
     struct tempName oldTn, mappedTn, unmappedTn;
     FILE *old, *mapped, *unmapped;
     char *line;
     int lineSize;
     char *fromDb, *toDb;
-    int ct = 0, errCt = 0;
-
+    int ct = -1, errCt = 0;
+    enum liftOverFileType lft;
     /* read in user data and save to file */
     makeTempName(&oldTn, HGLFT, ".user");
     old = mustOpen(oldTn.forCgi, "w");
     fputs(userData, old);
     fputs("\n", old);           /* in case user doesn't end last line */
     carefulClose(&old);
     chmod(oldTn.forCgi, 0666);
 
     /* setup output files -- one for converted lines, the other
      * for lines that could not be mapped */
     makeTempName(&mappedTn, HGLFT, ".bed");
     makeTempName(&unmappedTn, HGLFT, ".err");
     mapped = mustOpen(mappedTn.forCgi, "w");
     chmod(mappedTn.forCgi, 0666);
     unmapped = mustOpen(unmappedTn.forCgi, "w");
     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);
-    ct = liftOverBedOrPositions(oldTn.forCgi, 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);
+    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);
         printf("%s: ", ct > 1 ? "s" : "");
         printf("<A HREF=%s TARGET=_blank>View Conversions</A>\n", mappedTn.forCgi);
@@ -527,34 +534,36 @@
         /* some records not converted */
         cgiParagraph("");
         printf("Conversion failed on %d record", errCt);
         printf("%s. &nbsp;&nbsp;&nbsp;", errCt > 1 ? "s" : "");
         printf("<A HREF=%s TARGET=_blank>Display failure file</A>&nbsp; &nbsp;\n",
                          unmappedTn.forCgi);
         printf("<A HREF=\"../cgi-bin/hgLiftOver?%s=1\" TARGET=_blank>Explain failure messages</A>\n", HGLFT_ERRORHELP_VAR);
         puts("<P>Failed input regions:\n");
         struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE);
         puts("<BLOCKQUOTE><PRE>\n");
         while (lineFileNext(errFile, &line, &lineSize))
             puts(line);
         lineFileClose(&errFile);
         puts("</PRE></BLOCKQUOTE>\n");
         }
+    if ((multiple) && (lft == positions))
+	{
     puts("<BLOCKQUOTE><PRE>\n");
     puts("Note: &quot;multiple&quot; option is not supported for position format.");
     puts("</PRE></BLOCKQUOTE>\n");
-
+	}
     webParamsUsed(minMatch, multiple, minSizeQ, minChainT, minBlocks, fudgeThick);
 
     carefulClose(&unmapped);
     }
 webDownloads();
 cartWebEnd();
 }
 
 /* Null terminated list of CGI Variables we don't want to save
  * permanently. */
 char *excludeVars[] = {"Submit", "submit", "SubmitFile",
                         HGLFT_USERDATA_VAR,
                         HGLFT_DATAFILE_VAR,
                         HGLFT_ERRORHELP_VAR,
                         NULL};