src/utils/bigBedSummary/bigBedSummary.c 1.4

Index: src/utils/bigBedSummary/bigBedSummary.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bigBedSummary/bigBedSummary.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/utils/bigBedSummary/bigBedSummary.c	5 Feb 2009 20:49:48 -0000	1.3
+++ src/utils/bigBedSummary/bigBedSummary.c	15 Mar 2009 00:18:23 -0000	1.4
@@ -1,76 +1,113 @@
 /* bigBedSummary - Extract summary information from a bigBed file.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "sqlNum.h"
 #include "bigBed.h"
+#include "asParse.h"
 
 static char const rcsid[] = "$Id$";
 
 char *summaryType = "coverage";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigBedSummary - Extract summary information from a bigBed file.\n"
   "usage:\n"
   "   bigWigSummary file.bb chrom start end dataPoints\n"
   "Get summary data from bigBed 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"
   "         coverage - %% of region that is covered (default)\n"
   "         mean - average depth of covered regions\n"
   "         min - minimum depth of covered regions\n"
   "         max - maximum depth of covered regions\n"
+  "   -fields - print out information on fields in file.\n"
+  "      If fields option is used, the chrom, start, end, dataPoints\n"
+  "      parameters may be omitted\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"type", OPTION_STRING},
+   {"fields", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void bigBedSummary(char *fileName, char *chrom, int start, int end, int dataPoints)
 /* bigBedSummary - Extract summary information from a bigBed file.. */
 {
 /* Make up values array initialized to not-a-number. */
 double nan0 = nan("");
 double summaryValues[dataPoints];
 int i;
 for (i=0; i<dataPoints; ++i)
     summaryValues[i] = nan0;
 
-if (bigBedSummaryArray(fileName, chrom, start, end, bbiSummaryTypeFromString(summaryType), 
+struct bbiFile *bbi = bigBedFileOpen(fileName);
+if (bigBedSummaryArray(bbi, 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, fileName);
     }
+bbiFileClose(&bbi);
+}
+
+
+void bigBedFields(char *fileName)
+/* Print out info about fields in bed file. */
+{
+struct bbiFile *bbi = bigBedFileOpen(fileName);
+printf("%d bed definition fields, %d total fields\n", bbi->definedFieldCount, bbi->fieldCount);
+struct asObject *as = bigBedAs(bbi);
+if (as != NULL)
+    {
+    struct asColumn *col;
+    for (col = as->columnList; col != NULL; col = col->next)
+        {
+	printf("\t%s\t%s\n", col->name, col->comment);
+	}
+    }
+else
+    {
+    printf("No additional field information included.\n");
+    }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
-summaryType = optionVal("type", summaryType);
-if (argc != 6)
+if (optionExists("fields"))
+    {
+    if (argc < 2)
+        usage();
+    bigBedFields(argv[1]);
+    }
+else
+    {
+    summaryType = optionVal("type", summaryType);
+    if (argc != 6)
     usage();
-bigBedSummary(argv[1], argv[2], sqlUnsigned(argv[3]), sqlUnsigned(argv[4]), sqlUnsigned(argv[5]));
+    bigBedSummary(argv[1], argv[2], sqlUnsigned(argv[3]), sqlUnsigned(argv[4]), sqlUnsigned(argv[5]));
+    }
 return 0;
 }