15080c151c9929733fa2af71ce5dc98533c4f913
galt
  Fri Mar 20 18:45:40 2026 -0700
The error messages are more detailed to help users, something MarkD wanted.
It aborts by default if chromStart or chromEnd are greater than chromSize,
unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now.

Fixes issues with undetected overflowing integers issues, warns when they are too large
instead of silently failing. Expanded the all the coordinates in the utils and the lib
so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space.

I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities

bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig.
refs #28109

diff --git src/lib/bigBedCmdSupport.c src/lib/bigBedCmdSupport.c
index 92401e9a21e..d7f1cf59262 100644
--- src/lib/bigBedCmdSupport.c
+++ src/lib/bigBedCmdSupport.c
@@ -35,179 +35,261 @@
 
 void bigBedCmdOutputTsvHeader(struct bbiFile *bbi, FILE *f)
 /* output a TSV-style header from the autoSql in the file */
 {
 outputHeader(bbi, f, '\0');
 }
 
 struct hash *makeChromHash(struct bbiChromInfo *chromList)
 // make a fast searchable hash from chromList 
 {
 
 struct hash *chromHash = hashNew(10);
 struct bbiChromInfo *chrom;
 for (chrom = chromList; chrom != NULL; chrom = chrom->next)
     {
-    hashAdd(chromHash, cloneString(chrom->name), NULL);
+    hashAdd(chromHash, cloneString(chrom->name), chrom);
     }
 return chromHash;
 }
 
+void parsePositionIntoRows(char *position, char **row, struct lineFile *lf)
+/* parse position into row array. Free row[0] to release memory. */
+{
+char *chrom = cloneString(position);
+char *startStr = strchr(chrom, ':');
+if (startStr == NULL)
+    {
+    errAbort("required character colon (:) not found in input string position %s fileName=%s row number=%d",
+	position, lf->fileName, lf->lineIx);
+    }
+*startStr++ = '\0';
+if (isEmpty(chrom))
+    {
+    errAbort("chrom is not allowed to be empty in input string position %s fileName=%s row number=%d",
+	position, lf->fileName, lf->lineIx);
+    }
+char *endStr = strchr(startStr, '-');
+if (endStr == NULL)
+    {
+    errAbort("required character dash (-) not found in input string position %s fileName=%s row number=%d",
+	position, lf->fileName, lf->lineIx);
+    }
+*endStr++ = '\0';
+if (isEmpty(startStr))
+    {
+    errAbort("start %s is not allowed to be empty in input string position %s fileName=%s row number=%d",
+	startStr, position, lf->fileName, lf->lineIx);
+    }
+if (isEmpty(endStr))
+    {
+    errAbort("end %s is not allowed to be empty in input string position %s fileName=%s row number=%d",
+	endStr, position, lf->fileName, lf->lineIx);
+    }
+row[0] = chrom;
+row[1] = startStr;
+row[2] = endStr;
+}
 
-static struct bed *bed3FromPositionString(char *line)
+void lineFileAllIntsFieldNameAndLine(struct lineFile *lf, char *words[], int wordIx, char *fieldName, void *val,
+  boolean isSigned,  int byteCount, char *typeString, boolean noNeg, char *line)
+/* Returns long long integer from converting the input string. Aborts on error. */
+{
+char *s = words[wordIx];
+char errMsg[256];
+int res = lineFileCheckAllIntsNoAbort(s, val, isSigned, byteCount, typeString, noNeg, errMsg, sizeof errMsg);
+if (res > 0)
+    {
+    errAbort("%s in %s field %d line %d of %s, got %s in line %s",
+	errMsg, fieldName, wordIx+1, lf->lineIx, lf->fileName, s, line);
+    }
+}
+
+
+static struct bed *bed3FromPositionString(char *line, struct lineFile *lf)
 /* Read positions line and return bed 3. */
 {
-char *chrom;
-int start, end;
 struct bed *bed = NULL;
+char *row[3];
 
 /* Convert input to bed record */
-char *val = cloneString(line);
-mustParseRange(val, &chrom, &start, &end);  // does not subtract 1
-
-// 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);
+
+parsePositionIntoRows(line, row, lf);  
+
 AllocVar(bed);
-bed->chrom=cloneString(chrom);
-bed->chromStart=start;
-bed->chromEnd=end;
-freez(&val);
+bed->chrom=cloneString(row[0]);
+lineFileAllIntsFieldNameAndLine(lf, row, 1, "chromStart", &bed->chromStart, FALSE, 4, "integer", FALSE, line);
+lineFileAllIntsFieldNameAndLine(lf, row, 2, "chromEnd"  , &bed->chromEnd  , FALSE, 4, "integer", FALSE, line);
+
+if (bed->chromStart == 0)
+    errAbort("invalid position start = 0 since position starts at 1, fileName=%s row number=%d %s", lf->fileName, lf->lineIx, line);
+
+--bed->chromStart;
+
 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);
+    bed = bed3FromPositionString(line, lf);
     slAddHead(&bedList, bed);
     }
 lineFileClose(&lf);
 return bedList;
 }
 
 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 bed *list = NULL, *bed = NULL;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line, *row[bedKnownFields];
 
 while (lineFileNextReal(lf, &line))
     {
-    int numFields = chopByWhite(line, row, ArraySize(row));
+    char *val=cloneString(line);
+    int numFields = chopByWhite(val, 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));
+
+    AllocVar(bed);
+    bed->chrom = cloneString(row[0]);
+    lineFileAllIntsFieldNameAndLine(lf, row, 1, "chromStart", &bed->chromStart, FALSE, 4, "integer", FALSE, line);
+    lineFileAllIntsFieldNameAndLine(lf, row, 2, "chromEnd"  , &bed->chromEnd  , FALSE, 4, "integer", FALSE, line);
+    if (numFields >= 4)
+	bed->name = cloneString(row[3]);
+
+    slAddHead(&list, bed);
+
+    freeMem(val);
     }
 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
  * possibly multiple -range parameters.  Dispose of this with bedFreeList(). 
  */
 {
 struct slName *range = NULL;
 struct bed *bed, *list = NULL;
-char *row[bedKnownFields];
+char *row[3];
+
+// make fake lf to pass fileName and line number in error messages
+struct lineFile *lf=NULL;
+AllocVar(lf);
+lf->fileName=cloneString("range");
+lf->lineIx = 0;
 
 for(range=ranges; range; range=range->next)
     {
-    if (strchr(range->name, ':'))
+    ++lf->lineIx;
+    if (strchr(range->name, ':') || strchr(range->name, '-'))
         {
-        bed = bed3FromPositionString(range->name);
+        bed = bed3FromPositionString(range->name, lf);
         }
     else
         {
 	char *val=cloneString(range->name);
 	int numFields = chopByWhite(val, row, ArraySize(row));
 	if (numFields != 3)
 	    errAbort("range %s doesn't appear to be in bed format. 3 fields required, got %d", 
 		range->name, numFields);
-	bed = bedLoadN(row, numFields);
+	// copy column 1 as chromName clonestring
+	AllocVar(bed);
+	bed->chrom = cloneString(row[0]);
+	lineFileAllIntsFieldNameAndLine(lf, row, 1, "chromStart", &bed->chromStart, FALSE, 4, "integer", FALSE, range->name);
+	lineFileAllIntsFieldNameAndLine(lf, row, 2, "chromEnd"  , &bed->chromEnd  , FALSE, 4, "integer", FALSE, range->name);
 	freez(&val);
         }
     slAddHead(&list, bed);
     }
 slReverse(&list);
+freez(&lf->fileName);
+freez(&lf);
 return list;
 }
 
+static void checkBed(struct bed *bed, struct hash *chromHash)
+/* check a bed record */
+{
+if (chromHash && !hashLookup(chromHash, bed->chrom))
+    errAbort("invalid chrom = %s not found", bed->chrom);
+struct bbiChromInfo *chrom = NULL;
+if (chromHash && hashLookup(chromHash, bed->chrom))
+    chrom = (struct bbiChromInfo *) hashFindVal(chromHash, bed->chrom);
+
+// complain and abort over coords and chromSize
+if (chrom && (bed->chromStart > chrom->size))
+    errAbort("invalid start=%u > chromSize=%u", bed->chromStart, chrom->size);
+if (chrom && (bed->chromEnd > chrom->size))
+    errAbort("invalid end=%u > chromSize=%u", bed->chromEnd, chrom->size);
+
+if (bed->chromStart > bed->chromEnd)
+    errAbort("invalid range, start=%u > end=%u", bed->chromStart, bed->chromEnd);
+}
 
 void genericBigToNonBigFromBed(struct bbiFile *bbi, struct hash *chromHash, char *bedFileName, FILE *outFile, 
- void (*processChromChunk)(struct bbiFile *bbi, char *chrom, int start, int end, char *bedName, FILE *f)
+ void (*processChromChunk)(struct bbiFile *bbi, char *chrom, uint start, uint end, char *bedName, FILE *f)
 )
 /* Read list of ranges from bed file chrom start end.
  * Automatically sort them by chrom, start. If bed4 pass bed->name too. */
 {
 struct bed *bed, *bedList = bedLoad3Plus(bedFileName);
 slSort(&bedList, bedCmp);
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
-    if (chromHash && !hashLookup(chromHash, bed->chrom))
-	errAbort("invalid chrom = %s not found", bed->chrom);
-    if (bed->chromStart > bed->chromEnd)
-	errAbort("invalid range, start=%u > end=%u", bed->chromStart, bed->chromEnd);
+    checkBed(bed, chromHash);
     processChromChunk(bbi, bed->chrom, bed->chromStart, bed->chromEnd, bed->name, outFile);
     }
 bedFreeList(&bedList);
 }
 
 void genericBigToNonBigFromRange(struct bbiFile *bbi, struct hash *chromHash, FILE *outFile, struct slName *ranges,
- void (*processChromChunk)(struct bbiFile *bbi, char *chrom, int start, int end, char *bedName, FILE *f)
+ void (*processChromChunk)(struct bbiFile *bbi, char *chrom, uint start, uint end, char *bedName, FILE *f)
 )
 /* Read list of ranges as chrom start end or chrom:start-end.
  * Automatically sort them by chrom, start. */
 {
 struct bed *bed, *bedList = bedLoad3FromRangeOption(ranges);
 slSort(&bedList, bedCmp);
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
-    if (chromHash && !hashLookup(chromHash, bed->chrom))
-	errAbort("invalid chrom = %s not found", bed->chrom);
-    if (bed->chromStart > bed->chromEnd)
-	errAbort("invalid range, start=%u > end=%u", bed->chromStart, bed->chromEnd);
+    checkBed(bed, chromHash);
     processChromChunk(bbi, bed->chrom, bed->chromStart, bed->chromEnd, bed->name, outFile);
     }
 bedFreeList(&bedList);
 }
 
 
 void genericBigToNonBigFromPos(struct bbiFile *bbi, struct hash *chromHash, char *posFileName, FILE *outFile, 
- void (*processChromChunk)(struct bbiFile *bbi, char *chrom, int start, int end, char *bedName, FILE *f)
+ void (*processChromChunk)(struct bbiFile *bbi, char *chrom, uint start, uint end, char *bedName, FILE *f)
 )
 {
 /* Read  positions from file (chrom:start-end). starts are 1-based,
  * but after conversion to bed3 list, they are 0-based. 
  * Automatically sort them by chrom, start */
 struct bed *bed, *bedList = bed3FromPositions(posFileName);
 
 slSort(&bedList, bedCmp);
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
-    if (chromHash && !hashLookup(chromHash, bed->chrom))
-	errAbort("invalid chrom = %s not found", bed->chrom);
-    if (bed->chromStart > bed->chromEnd)
-	errAbort("invalid range, start=%u > end=%u", bed->chromStart, bed->chromEnd);
+    checkBed(bed, chromHash);
     processChromChunk(bbi, bed->chrom, bed->chromStart, bed->chromEnd, NULL, outFile);
     }
 bedFreeList(&bedList);
 }