d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6
galt
  Fri Feb 13 18:23:42 2026 -0800
Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925

diff --git src/inc/bigBedCmdSupport.h src/inc/bigBedCmdSupport.h
index 238a3c0dfca..42838f51125 100644
--- src/inc/bigBedCmdSupport.h
+++ src/inc/bigBedCmdSupport.h
@@ -1,32 +1,43 @@
 /* bigBedCmdSupport - functions to support writing bigBed related commands. */
 
 /* Copyright (C) 2022 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef bigBedCmdSupport_h
 #define bigBedCmdSupport_h
 #include "bigBed.h"
 
 void bigBedCmdOutputHeader(struct bbiFile *bbi, FILE *f);
 /* output a autoSql-style header from the autoSql in the file */
 
 void bigBedCmdOutputTsvHeader(struct bbiFile *bbi, FILE *f);
 /* output a TSV-style header from the autoSql in the file */
 
+struct hash *makeChromHash(struct bbiChromInfo *chromList);
+/* make a fast searchable hash from chromList */
+
 struct bed *bed3FromPositions(char *fileName);
 /* Read positions file and retrun bed 3 list. */
 
-void genericBigToNonBigFromBed(struct bbiFile *bbi, char *bedFileName, FILE *outFile, 
+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)
 );
 /* Read list of ranges from bed file chrom start end.
  * Automatically sort them by chrom, start */
 
-void genericBigToNonBigFromPos(struct bbiFile *bbi, char *posFileName, FILE *outFile, 
+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)
+);
+/* Read list of ranges from commandline option as chrom start end or chrom:start-end.
+ * Supports multiple -range options.
+ * Automatically sort them by chrom, start. */
+
+
+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)
 );
 /* 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 */
 
 #endif