61dc7885a5f1001e2bc189501379088f2b53379d
galt
  Mon Feb 23 15:42:36 2026 -0800
fixes things found automated codereview. for bigBedCmdSupport lib moved slAddHead, removed stray debugmsg and fixed comment and added static keyword. fixed bigChainToChain chromFound = FALSE, removed stray test makefile, fixed existing typo "tines", and added a missing space after issing space before optionMultiVal(). refs #37146

diff --git src/lib/bigBedCmdSupport.c src/lib/bigBedCmdSupport.c
index 32235727e69..92401e9a21e 100644
--- src/lib/bigBedCmdSupport.c
+++ src/lib/bigBedCmdSupport.c
@@ -51,91 +51,89 @@
     }
 return chromHash;
 }
 
 
 static struct bed *bed3FromPositionString(char *line)
 /* Read positions line and return bed 3. */
 {
 char *chrom;
 int start, end;
 struct bed *bed = NULL;
 
 /* Convert input to bed record */
 char *val = cloneString(line);
 mustParseRange(val, &chrom, &start, &end);  // does not subtract 1
- verbose(1,"bed3FromPositionString after mustParseRange chrom=%s\n", chrom);
 
 // used to use parseRegion which checks for overflow,
 // but only catches start < 1 because of integer overflow.
 if (start < 1)
     errAbort("invalid range, start=%d < 1, but first base is 1 or more", start);
 --start;
 if (start > end)
     errAbort("invalid range, (start - 1)=%d > end=%d", start, end);
 AllocVar(bed);
 bed->chrom=cloneString(chrom);
 bed->chromStart=start;
 bed->chromEnd=end;
 freez(&val);
 return bed;
 }
 
 
 struct bed *bed3FromPositions(char *fileName)
 /* Read positions file and retrun bed 3 list. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct bed *bed = NULL, *bedList = NULL;
 char *line;
 
 /* Convert input to bed file */
 while (lineFileNextReal(lf, &line))
     {
     bed = bed3FromPositionString(line);
-    }
     slAddHead(&bedList, bed);
+    }
 lineFileClose(&lf);
 return bedList;
 }
 
-struct bed *bedLoad3Plus(char *fileName)
+static struct bed *bedLoad3Plus(char *fileName)
 /* Determines how many fields are in a bedFile and load all beds from
  * a tab-separated file.  Dispose of this with bedFreeList(). 
  * Small change by Michael to require only 3 or more fields. Meaning we will accept bed3 
  */
 {
 struct bed *list = NULL;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line, *row[bedKnownFields];
 
 while (lineFileNextReal(lf, &line))
     {
     int numFields = chopByWhite(line, row, ArraySize(row));
     if (numFields < 3)
 	errAbort("file %s doesn't appear to be in bed format. At least 3 fields required, got %d", fileName, numFields);
     slAddHead(&list, bedLoadN(row, numFields));
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bed *bedLoad3FromRangeOption(struct slName *ranges)
 /* Determines how many fields are in a bedFile and load all beds from
- * a tab-separated file.  Dispose of this with bedFreeList(). 
- * Small change by Michael to require only 3 or more fields. Meaning we will accept bed3 
+ * possibly multiple -range parameters.  Dispose of this with bedFreeList(). 
  */
 {
 struct slName *range = NULL;
 struct bed *bed, *list = NULL;
 char *row[bedKnownFields];
 
 for(range=ranges; range; range=range->next)
     {
     if (strchr(range->name, ':'))
         {
         bed = bed3FromPositionString(range->name);
         }
     else
         {
 	char *val=cloneString(range->name);