04b879361227c44e9602945464b83e5346b5dd4f
markd
  Tue Jul 19 22:38:07 2022 -0700
add option to output autoSql style header to bigBedNamedItems

diff --git src/utils/bigBedToBed/bigBedToBed.c src/utils/bigBedToBed/bigBedToBed.c
index 09edda0..eef6593 100644
--- src/utils/bigBedToBed/bigBedToBed.c
+++ src/utils/bigBedToBed/bigBedToBed.c
@@ -1,28 +1,29 @@
 /* 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"
 
 
 char *clChrom = NULL;
 int clStart = -1;
 int clEnd = -1;
 int maxItems = 0;
 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"
@@ -35,54 +36,37 @@
   "   -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},
    {"udcDir", OPTION_STRING},
    {"header", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 
-void writeHeader(struct bbiFile *bbi, FILE *f)
-/* output a header from the autoSql in the file */
-{
-char *asText = bigBedAutoSqlText(bbi);
-if (asText == NULL)
-    errAbort("bigBed files does not contain an autoSql schema");
-struct asObject *asObj = asParseText(asText);
-char sep = '#';
-for (struct asColumn *asCol = asObj->columnList; asCol != NULL; asCol = asCol->next)
-    {
-    fputc(sep, f);
-    fputs(asCol->name, f);
-    sep = '\t';
-    }
-fputc('\n', f);
-}
-
 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)
-    writeHeader(bbi, f);
+    bigBedCmdOutputHeader(bbi, f);
 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)
         {