e2389e03c44ae29a330fd0234060494246cb41c5
max
  Wed Jun 28 08:12:06 2023 +0200
now adding the source code change for -bed option to bigBedToBed, refs #31531

diff --git src/utils/bigBedToBed/bigBedToBed.c src/utils/bigBedToBed/bigBedToBed.c
index eef6593..10f5065 100644
--- src/utils/bigBedToBed/bigBedToBed.c
+++ src/utils/bigBedToBed/bigBedToBed.c
@@ -1,112 +1,130 @@
 /* bigBedToBed - Convert from bigBed to ascii bed format.. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "localmem.h"
 #include "udc.h"
 #include "bigBed.h"
 #include "asParse.h"
 #include "obscure.h"
 #include "bigBedCmdSupport.h"
+#include "basicBed.h"
 
 
 char *clChrom = NULL;
 int clStart = -1;
 int clEnd = -1;
-int maxItems = 0;
+char *clBed = NULL;
 boolean header = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigBedToBed v1 - Convert from bigBed to ascii bed format.\n"
   "usage:\n"
   "   bigBedToBed input.bb output.bed\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"
-  "   -maxItems=N - if set, restrict output to first N items\n"
+  "   -end=N - if set, restrict output to only that under end\n"
+  "   -bed=in.bed - restrict output to all regions in a BED file\n"
   "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
   "   -header - output a autoSql-style header (starts with '#').\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"chrom", OPTION_STRING},
    {"start", OPTION_INT},
    {"end", OPTION_INT},
-   {"maxItems", OPTION_INT},
+   {"bed", OPTION_STRING},
    {"udcDir", OPTION_STRING},
    {"header", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
+static void writeFeatures(struct bbiFile *bbi, char *chromName, int start, int end, int itemsLeft, struct lm *lm, FILE *f)
+{
+    struct bigBedInterval *interval, *intervalList = bigBedIntervalQuery(bbi, chromName, 
+    	start, end, itemsLeft, lm);
+    for (interval = intervalList; interval != NULL; interval = interval->next)
+	{
+	fprintf(f, "%s\t%u\t%u", chromName, interval->start, interval->end);
+	char *rest = interval->rest;
+	if (rest != NULL)
+	    fprintf(f, "\t%s\n", rest);
+	else
+	    fprintf(f, "\n");
+	}
+}
+
+static void bigBedToBedFromBed(struct bbiFile *bbi, char *bedFileName, FILE *outFile)
+{
+struct bed *bed, *bedList = bedLoadNAll(bedFileName, 3);
+int itemsLeft = 0;
+struct lm *lm = lmInit(0);
+for (bed = bedList; bed != NULL; bed = bed->next)
+    {
+    writeFeatures(bbi, bed->chrom, bed->chromStart, bed->chromEnd, itemsLeft, lm, outFile);
+    }
+lmCleanup(&lm);
+}
 
 void bigBedToBed(char *inFile, char *outFile)
 /* bigBedToBed - Convert from bigBed to ascii bed format.. */
 {
 struct bbiFile *bbi = bigBedFileOpen(inFile);
 FILE *f = mustOpen(outFile, "w");
 if (header)
     bigBedCmdOutputHeader(bbi, f);
+
+if (clBed != NULL)
+    {
+    bigBedToBedFromBed(bbi, clBed, f);
+    return;
+    }
+
 struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
 int itemCount = 0;
 for (chrom = chromList; chrom != NULL; chrom = chrom->next)
     {
     if (clChrom != NULL && !sameString(clChrom, chrom->name))
         continue;
     char *chromName = chrom->name;
     int start = 0, end = chrom->size;
     if (clStart > 0)
         start = clStart;
     if (clEnd > 0)
         end = clEnd;
     int itemsLeft = 0;	// Zero actually means no limit.... 
-    if (maxItems != 0)
-        {
-	itemsLeft = maxItems - itemCount;
-	if (itemsLeft <= 0)
-	    break;
-	}
     struct lm *lm = lmInit(0);
-    struct bigBedInterval *interval, *intervalList = bigBedIntervalQuery(bbi, chromName, 
-    	start, end, itemsLeft, lm);
-    for (interval = intervalList; interval != NULL; interval = interval->next)
-	{
-	fprintf(f, "%s\t%u\t%u", chromName, interval->start, interval->end);
-	char *rest = interval->rest;
-	if (rest != NULL)
-	    fprintf(f, "\t%s\n", rest);
-	else
-	    fprintf(f, "\n");
-	}
+    writeFeatures(bbi, chromName, start, end, itemsLeft, lm, f);
     lmCleanup(&lm);
     }
 bbiChromInfoFreeList(&chromList);
 carefulClose(&f);
 bbiFileClose(&bbi);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 clChrom = optionVal("chrom", clChrom);
 clStart = optionInt("start", clStart);
 clEnd = optionInt("end", clEnd);
-maxItems = optionInt("maxItems", maxItems);
+clBed = optionVal("bed", clBed);
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 header = optionExists("header");
 if (argc != 3)
     usage();
 bigBedToBed(argv[1], argv[2]);
 if (verboseLevel() > 1)
     printVmPeak();
 return 0;
 }