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/hg/utils/bigPslToPsl/bigPslToPsl.c src/hg/utils/bigPslToPsl/bigPslToPsl.c
index 8a60b4ac527..33e93b96468 100644
--- src/hg/utils/bigPslToPsl/bigPslToPsl.c
+++ src/hg/utils/bigPslToPsl/bigPslToPsl.c
@@ -1,149 +1,177 @@
 /* bigPslToPsl - convert bigPsl file to psl. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "obscure.h"
 #include "bigBed.h"
 #include "psl.h"
 #include "bigPsl.h"
 #include "basicBed.h"
 #include "bigBedCmdSupport.h"
 
 char *clChrom = NULL;
 int clStart = -1;
 int clEnd = -1;
 char *clBed = NULL;
 char *clPos = NULL;
+struct slName *clRange = NULL;
+struct hash *chromHash = NULL;
+boolean skipChromCheck = FALSE;
 
 int seqTypeField = 0;
 
 struct lm *lm = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigPslToPsl - convert bigPsl file to psl\n"
   "usage:\n"
   "   bigPslToPsl bigPsl.bb output.psl\n"
   "options:\n"
   "   -chrom=chr1 - if set restrict output to given chromosome\n"
   "   -start=N - if set, restrict output to only that over start\n"
   "   -end=N - if set, restict output to only that under end\n"
+  "   -range=\"chrom start end\" - if set, restrict output to only that within range from start to end. \n"
+  "          This range start is a half-open 0-based coordinate like used in BED files. \n"
+  "   -range=chrom:start-end - if set, restrict output to only that within range from start to end. \n"
+  "          This range start is a 1-based start position. \n"
+  "    Do not use range with chrom, start, and/or end options. \n"
+  "   -range may be specified multiple times for multiple ranges. \n"
   "   -bed=in.bed - restrict output to all regions in a BED file\n"
   "   -positions=in.pos - restrict output to all regions in a position file with 1-based start\n"
   "   -collapseStrand   if target strand is '+', don't output it\n"
   "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
+  "   -skipChromCheck - skip checking chrom name.\n"
   );
 }
 
 boolean collapseStrand = FALSE;
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"chrom", OPTION_STRING},
    {"start", OPTION_INT},
    {"end", OPTION_INT},
    {"bed", OPTION_STRING},
+   {"range", OPTION_STRING|OPTION_MULTI},
    {"positions", OPTION_STRING},
    {"collapseStrand", OPTION_BOOLEAN},
    {"udcDir", OPTION_STRING},
+   {"skipChromCheck", OPTION_BOOLEAN},
     {NULL, 0},
 };
 
 static void processChromChunk(struct bbiFile *bbi, char *chrom,
                               int start, int end, char *bedName, FILE *f)
 /* Output one chunk.  Only blocks where start is in the range will be written
  * to avoid outputting a block multiple tines.  */
 {
 int itemsLeft = 0;
 char *chromName = chrom;
 
 struct bigBedInterval  *bbList = bigBedIntervalQuery(bbi, chromName,
 	start, end, itemsLeft, lm);
 
 for(; bbList; bbList = bbList->next)
     {
     struct psl *psl, *pslList = pslFromBigPsl(chromName, bbList, seqTypeField, NULL, NULL);
 
     for(psl=pslList; psl; psl = psl->next)
 	{
 	if (collapseStrand && (psl->strand[1] == '+'))
 	    psl->strand[1] = 0;
 	pslTabOut(psl, f);
 	}
     }
 
 }
 
 
 void bigPslToPsl(char *bigPslName, char *outputName)
 /* bigPslToPsl - convert bigPsl file to psle. */
 {
 struct bbiFile *bbi = bigBedFileOpen(bigPslName);
 FILE *f = mustOpen(outputName, "w");
+struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
 seqTypeField =  bbExtraFieldIndex(bbi, "seqType");
+if (!skipChromCheck)
+    chromHash = makeChromHash(chromList);
 if (clBed != NULL)
     {
-    genericBigToNonBigFromBed(bbi, clBed, f, &processChromChunk);
-    return;
+    genericBigToNonBigFromBed(bbi, chromHash, clBed, f, &processChromChunk);
     }
-if (clPos != NULL)
+else if (clPos != NULL)
     {
-    genericBigToNonBigFromPos(bbi, clPos, f, &processChromChunk);
-    return;
+    genericBigToNonBigFromPos(bbi, chromHash, clPos, f, &processChromChunk);
     }
-struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
+else if (clRange != NULL)
+    {
+    genericBigToNonBigFromRange(bbi, chromHash, f, clRange, &processChromChunk);
+    }
+else
+    {
+    boolean chromFound = FALSE;
     for (chrom = chromList; chrom != NULL; chrom = chrom->next)
 	{
 
 	if (clChrom != NULL && !sameString(clChrom, chrom->name))
 	    continue;
 
+	chromFound = TRUE;
 	int start = 0, end = chrom->size;
 	if (clStart >= 0)
 	    start = clStart;
 	if (clEnd >= 0)
 	    {
 	    end = clEnd;
 	    if (end > chrom->size)
 		end = chrom->size;
 	    }
 	if (start > end)
 	    errAbort("invalid range, start=%d > end=%d", start, end);
 
 	processChromChunk(bbi, chrom->name, start, end, NULL, f);
 	}
+    if (clChrom && !chromFound && !skipChromCheck)
+	errAbort("specified chrom %s not found in bigPsl", clChrom);
+    }
+bbiChromInfoFreeList(&chromList);
+carefulClose(&f);
+bbiFileClose(&bbi);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 lm = lmInit(0);
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 clChrom = optionVal("chrom", clChrom);
 clStart = optionInt("start", clStart);
 clEnd = optionInt("end", clEnd);
 clBed = optionVal("bed", clBed);
+clRange =optionMultiVal("range", clRange);
 clPos = optionVal("positions", clPos);
 collapseStrand = optionExists("collapseStrand");
+skipChromCheck = optionExists("skipChromCheck");
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 
 if (argc != 3)
     usage();
 
-if ((clBed || clPos) && (clChrom || (clStart >= 0) || (clEnd >= 0)))
-    errAbort("-bed or -positions can not be used with -chrom -start or -end options");
-if (clBed && clPos)
-    errAbort("-bed and -positions can not be used together");
+if ((clBed || clPos || clRange) && (clChrom || (clStart >= 0) || (clEnd >= 0)))
+    errAbort("-bed or -positions or -range can not be used with -chrom -start or -end options");
+if ((clBed && clPos) || (clBed && clRange) || (clPos && clRange))
+    errAbort("-bed, -positions, and -range can not be used together");
 
 bigPslToPsl(argv[1], argv[2]);
 
 lmCleanup(&lm);
 if (verboseLevel() > 1)
     printVmPeak();
 return 0;
 }