src/utils/bigBedInfo/bigBedInfo.c 1.1

Index: src/utils/bigBedInfo/bigBedInfo.c
===================================================================
RCS file: src/utils/bigBedInfo/bigBedInfo.c
diff -N src/utils/bigBedInfo/bigBedInfo.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/utils/bigBedInfo/bigBedInfo.c	5 Nov 2009 19:57:31 -0000	1.1
@@ -0,0 +1,78 @@
+/* bigBedInfo - Show information about a bigBed file.. */
+#include "common.h"
+#include "linefile.h"
+#include "hash.h"
+#include "options.h"
+#include "udc.h"
+#include "bbiFile.h"
+#include "bigBed.h"
+#include "hmmstats.h"
+
+static char const rcsid[] = "$Id$";
+
+void usage()
+/* Explain usage and exit. */
+{
+errAbort(
+  "bigBedInfo - Show information about a bigBed file.\n"
+  "usage:\n"
+  "   bigBedInfo file.bb\n"
+  "options:\n"
+  "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
+  "   -chroms - list all chromosomes and their sizes\n"
+  "   -as - get autoSql spec\n"
+  );
+}
+
+static struct optionSpec options[] = {
+   {"udcDir", OPTION_STRING},
+   {"chroms", OPTION_BOOLEAN},
+   {"as", OPTION_BOOLEAN},
+   {NULL, 0},
+};
+
+void bigBedInfo(char *fileName)
+/* bigBedInfo - Show information about a bigBed file.. */
+{
+struct bbiFile *bbi = bigBedFileOpen(fileName);
+printf("version: %d\n", bbi->version);
+printf("isSwapped: %d\n", bbi->isSwapped);
+printf("itemCount: %lld\n", bigBedItemCount(bbi));
+printf("zoomLevels: %d\n", bbi->zoomLevels);
+struct bbiZoomLevel *zoom;
+for (zoom = bbi->levelList; zoom != NULL; zoom = zoom->next)
+    printf("\t%d\n", zoom->reductionLevel);
+struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
+printf("chromCount: %d\n", slCount(chromList));
+if (optionExists("chroms"))
+    for (chrom=chromList; chrom != NULL; chrom = chrom->next)
+	printf("\t%s %d %d\n", chrom->name, chrom->id, chrom->size);
+if (optionExists("as"))
+    {
+    char *asText = bigBedAutoSqlText(bbi);
+    if (asText == NULL)
+        printf("as:  n/a\n");
+    else
+	{
+	printf("as:\n");
+	printf("%s", asText);
+	}
+    }
+struct bbiSummaryElement sum = bbiTotalSummary(bbi);
+printf("basesCovered: %lld\n", sum.validCount);
+printf("meanDepth (of bases covered): %f\n", sum.sumData/sum.validCount);
+printf("minDepth: %f\n", sum.minVal);
+printf("maxDepth: %f\n", sum.maxVal);
+printf("std of depth: %f\n", calcStdFromSums(sum.sumData, sum.sumSquares, sum.validCount));
+}
+
+int main(int argc, char *argv[])
+/* Process command line. */
+{
+optionInit(&argc, argv, options);
+if (argc != 2)
+    usage();
+udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
+bigBedInfo(argv[1]);
+return 0;
+}