97d9ef321d57124ba40826c384e6a50a48e844dd
angie
  Wed Dec 7 14:44:01 2011 -0800
Thanks Brian for catching the "need to warn here" loose end in code review --now there is an actual warning.  I also updated bam.c to have the same
maxOut improvements as vcf.c.
Unfortunately, we still have the problem that several layers of code will
have to be modified in order to have genome-wide maxOut instead of per-region,
for non-wiggle data types.

diff --git src/hg/hgTables/vcf.c src/hg/hgTables/vcf.c
index 2929c86..511523e 100644
--- src/hg/hgTables/vcf.c
+++ src/hg/hgTables/vcf.c
@@ -319,57 +319,63 @@
     {
     vcfRecordToRow(rec, region->chrom, numBuf, dyAlt, dyFilter, dyInfo, dyGt, row);
     if (asFilterOnRow(filter, row))
         {
 	if ((idHash != NULL) && (hashLookup(idHash, rec->name) == NULL))
 	    continue;
 	struct bed *bed;
 	lmAllocVar(bedLm, bed);
 	bed->chrom = lmCloneString(bedLm, region->chrom);
 	bed->chromStart = rec->chromStart;
 	bed->chromEnd = rec->chromEnd;
 	bed->name = lmCloneString(bedLm, rec->name);
 	slAddHead(pBedList, bed);
 	}
     (*pMaxOut)--;
+    if (*pMaxOut <= 0)
+	break;
     }
 dyStringFree(&dyAlt);  dyStringFree(&dyFilter);  dyStringFree(&dyInfo);  dyStringFree(&dyGt);
 lmCleanup(&lm);
 vcfFileFree(&vcff);
 }
 
 struct bed *vcfGetFilteredBedsOnRegions(struct sqlConnection *conn,
 	char *db, char *table, struct region *regionList, struct lm *lm,
 	int *retFieldCount)
 /* Get list of beds from VCF, in all regions, that pass filtering. */
 {
 int maxOut = bigFileMaxOutput();
 /* Figure out vcf file name get column info and filter. */
 struct asObject *as = vcfAsObj();
 struct asFilter *filter = asFilterFromCart(cart, db, table, as);
 struct hash *idHash = identifierHash(db, table);
 
 /* Get beds a region at a time. */
 struct bed *bedList = NULL;
 struct region *region;
 for (region = regionList; region != NULL; region = region->next)
     {
     char *fileName = vcfFileName(table, conn, region->chrom);
     addFilteredBedsOnRegion(fileName, region, table, filter, lm, &bedList, idHash, &maxOut);
     freeMem(fileName);
     if (maxOut <= 0)
-	break; //#*** need to warn here
+	{
+	warn("Reached output limit of %d data values, please make region smaller,\n"
+	     "\tor set a higher output line limit with the filter settings.", bigFileMaxOutput());
+	break;
+	}
     }
 slReverse(&bedList);
 return bedList;
 }
 
 struct slName *randomVcfIds(char *table, struct sqlConnection *conn, int count)
 /* Return some semi-random IDs from a VCF file. */
 {
 /* Read 10000 items from vcf file,  or if they ask for a big list, then 4x what they ask for. */
 char *fileName = vcfFileName(table, conn, NULL);
 struct lineFile *lf = lineFileTabixMayOpen(fileName, TRUE);
 if (lf == NULL)
     noWarnAbort();
 int orderedCount = count * 4;
 if (orderedCount < 10000)