src/utils/bedToBigBed/bedToBigBed.c 1.2

Index: src/utils/bedToBigBed/bedToBigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bedToBigBed/bedToBigBed.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/utils/bedToBigBed/bedToBigBed.c	1 Feb 2009 02:28:46 -0000	1.1
+++ src/utils/bedToBigBed/bedToBigBed.c	10 Feb 2009 22:11:00 -0000	1.2
@@ -1,52 +1,57 @@
 /* bedToBigBed - Convert bed file to bigBed.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "bigBed.h"
 
 static char const rcsid[] = "$Id$";
 
 int blockSize = 1024;
 int itemsPerSlot = 64;
+int bedFields = 0;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bedToBigBed - Convert bed file to bigBed.\n"
   "usage:\n"
   "   bedToBigBed in.bed chrom.sizes out.bb\n"
   "Where in.bed is in one of the ascii bed formats, but not including track lines\n"
   "and chrom.sizes is two column: <chromosome name> <size in bases>\n"
   "and out.bb is the output indexed big bed file.\n"
   "options:\n"
   "   -blockSize=N - Number of items to bundle in r-tree.  Default %d\n"
   "   -itemsPerSlot=N - Number of data points bundled at lowest level. Default %d\n"
+  "   -bedFields=N - Number of fields that fit standard bed definition.  If undefined\n"
+  "                  assumes all fields in bed are defined.\n"
   , blockSize, itemsPerSlot
   );
 }
 
 static struct optionSpec options[] = {
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
+   {"bedFields", OPTION_INT},
    {NULL, 0},
 };
 
 void bedToBigBed(char *inName, char *chromSizes, char *outName)
 /* bedToBigBed - Convert bed file to bigBed.. */
 {
-bigBedFileCreate(inName, chromSizes, blockSize, itemsPerSlot, outName);
+bigBedFileCreate(inName, chromSizes, blockSize, itemsPerSlot, bedFields, outName);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 blockSize = optionInt("blockSize", blockSize);
 itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
+bedFields = optionInt("bedFields", bedFields);
 if (argc != 4)
     usage();
 bedToBigBed(argv[1], argv[2], argv[3]);
 return 0;
 }