src/utils/bigWigSummary/bigWigSummary.c 1.13

Index: src/utils/bigWigSummary/bigWigSummary.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bigWigSummary/bigWigSummary.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 1000000 -r1.12 -r1.13
--- src/utils/bigWigSummary/bigWigSummary.c	10 Nov 2009 05:46:36 -0000	1.12
+++ src/utils/bigWigSummary/bigWigSummary.c	20 Nov 2009 17:12:17 -0000	1.13
@@ -1,84 +1,85 @@
 /* bigWigSummary - Extract summary information from a bigWig file.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "sqlNum.h"
 #include "udc.h"
 #include "bigWig.h"
 
 static char const rcsid[] = "$Id$";
 
 char *summaryType = "mean";
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigWigSummary - Extract summary information from a bigWig file.\n"
   "usage:\n"
   "   bigWigSummary file.bigWig chrom start end dataPoints\n"
   "Get summary data from bigWig for indicated region, broken into\n"
   "dataPoints equal parts.  (Use dataPoints=1 for simple summary.)\n"
   "options:\n"
   "   -type=X where X is one of:\n"
   "         mean - average value in region (default)\n"
   "         min - minimum value in region\n"
   "         max - maximum value in region\n"
+  "         std - standard deviation in region\n"
   "         coverage - %% of region that is covered\n"
   "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"type", OPTION_STRING},
    {"udcDir", OPTION_STRING},
    {NULL, 0},
 };
 
 void bigWigSummary(char *bigWigFile, char *chrom, int start, int end, int dataPoints)
 /* bigWigSummary - Extract summary information from a bigWig file.. */
 {
 struct bbiFile *bwf = bigWigFileOpen(bigWigFile);
 
 /* Make up values array initialized to not-a-number. */
 double nan0 = strtod("NaN", NULL);
 double summaryValues[dataPoints];
 int i;
 for (i=0; i<dataPoints; ++i)
     summaryValues[i] = nan0;
 
 if (bigWigSummaryArray(bwf, chrom, start, end, bbiSummaryTypeFromString(summaryType), 
       dataPoints, summaryValues))
     {
     for (i=0; i<dataPoints; ++i)
 	{
 	double val = summaryValues[i];
 	if (i != 0)
 	    printf("\t");
 	if (isnan(val))
 	    printf("n/a");
 	else
 	    printf("%g", val);
 	}
     printf("\n");
     }
 else
     {
     errAbort("no data in region %s:%d-%d in %s\n", chrom, start, end, bigWigFile);
     }
 bigWigFileClose(&bwf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 6)
     usage();
 summaryType = optionVal("type", summaryType);
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 bigWigSummary(argv[1], argv[2], sqlUnsigned(argv[3]), sqlUnsigned(argv[4]), sqlUnsigned(argv[5]));
 return 0;
 }