src/utils/bedToBigBed/bedToBigBed.c 1.6

1.6 2009/05/13 01:13:57 kent
Adding clip parameter to bigBed creation. Making a few functions static that don't seem to need to be exposed at the moment.

Index: src/utils/bedToBigBed/bedToBigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bedToBigBed/bedToBigBed.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 4 -r1.5 -r1.6
--- src/utils/bedToBigBed/bedToBigBed.c	29 Apr 2009 17:50:36 -0000	1.5
+++ src/utils/bedToBigBed/bedToBigBed.c	13 May 2009 01:13:57 -0000	1.6
@@ -31,8 +31,10 @@
   "   -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 wig\n"
+  "                  file contains items off end of chromosome."
   , blockSize, itemsPerSlot
   );
 }
 
@@ -40,15 +42,17 @@
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
    {"bedFields", OPTION_INT},
    {"as", OPTION_STRING},
+   {"clip", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void bedToBigBed(char *inName, char *chromSizes, char *outName)
 /* bedToBigBed - Convert bed file to bigBed.. */
 {
-bigBedFileCreate(inName, chromSizes, blockSize, itemsPerSlot, bedFields, as, outName);
+bigBedFileCreate(inName, chromSizes, blockSize, itemsPerSlot, bedFields, as, 
+	optionExists("clip"), outName);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */