src/utils/bedToBigBed/bedToBigBed.c 1.5

Index: src/utils/bedToBigBed/bedToBigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bedToBigBed/bedToBigBed.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/utils/bedToBigBed/bedToBigBed.c	20 Apr 2009 23:17:26 -0000	1.4
+++ src/utils/bedToBigBed/bedToBigBed.c	29 Apr 2009 17:50:36 -0000	1.5
@@ -10,9 +10,8 @@
 int blockSize = 1024;
 int itemsPerSlot = 64;
 int bedFields = 0;
 char *as = NULL;
-boolean sorted = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
@@ -22,16 +21,18 @@
   "   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"
+  "If the input file is not sorted then this will sort the file in memory,\n"
+  "so it will run slightly faster if the input file is already sorted.\n"
+  "\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"
   "   -as=fields.as - If have non-standard fields, it's great to put a definition of\n"
   "                   each field in a row in AutoSql format here.\n"
-  "   -sorted       - Input is already sorted (quicker for very large files)\n"
   , blockSize, itemsPerSlot
   );
 }
 
@@ -39,16 +40,15 @@
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
    {"bedFields", OPTION_INT},
    {"as", OPTION_STRING},
-   {"sorted", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void bedToBigBed(char *inName, char *chromSizes, char *outName)
 /* bedToBigBed - Convert bed file to bigBed.. */
 {
-bigBedFileCreateDetailed(inName, sorted, chromSizes, blockSize, itemsPerSlot, bedFields, as, outName);
+bigBedFileCreate(inName, chromSizes, blockSize, itemsPerSlot, bedFields, as, outName);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
@@ -56,9 +56,8 @@
 optionInit(&argc, argv, options);
 blockSize = optionInt("blockSize", blockSize);
 itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
 bedFields = optionInt("bedFields", bedFields);
-sorted = optionExists("sorted");
 as = optionVal("as", as);
 if (argc != 4)
     usage();
 bedToBigBed(argv[1], argv[2], argv[3]);