src/utils/bedToBigBed/bedToBigBed.c 1.9

Index: src/utils/bedToBigBed/bedToBigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bedToBigBed/bedToBigBed.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 4 -r1.8 -r1.9
--- src/utils/bedToBigBed/bedToBigBed.c	18 Aug 2009 21:39:13 -0000	1.8
+++ src/utils/bedToBigBed/bedToBigBed.c	10 Sep 2009 01:49:22 -0000	1.9
@@ -36,10 +36,8 @@
   "   -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"
-  "   -clip - If set just issue warning messages rather than dying if bed\n"
-  "                  file contains items off end of chromosome."
   , blockSize, itemsPerSlot
   );
 }
 
@@ -47,9 +45,8 @@
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
    {"bedFields", OPTION_INT},
    {"as", OPTION_STRING},
-   {"clip", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void writeBlocks(struct bbiChromUsage *usageList, struct lineFile *lf, struct asObject *as, 
@@ -364,9 +361,8 @@
 	int itemsPerSlot, /* Number of items in lowest level of tree.  64 is good. */
 	bits16 definedFieldCount,  /* Number of defined bed fields - 3-16 or so.  0 means all fields
 				    * are the defined bed ones. */
 	char *asFileName, /* If non-null points to a .as file that describes fields. */
-	boolean clip,     /* If set silently clip out of bound coordinates. */
 	char *outName)    /* BigBed output file name. */
 /* Convert tab-separated bed file to binary indexed, zoomed bigBed version. */
 {
 /* Set up timing measures. */
@@ -564,9 +560,9 @@
 void bedToBigBed(char *inName, char *chromSizes, char *outName)
 /* bedToBigBed - Convert bed file to bigBed.. */
 {
 bbFileCreate(inName, chromSizes, blockSize, itemsPerSlot, bedFields, as, 
-	optionExists("clip"), outName);
+	outName);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */