e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/utils/bigBedInfo/bigBedInfo.c src/utils/bigBedInfo/bigBedInfo.c
index cfb9670..16f6eb2 100644
--- src/utils/bigBedInfo/bigBedInfo.c
+++ src/utils/bigBedInfo/bigBedInfo.c
@@ -1,133 +1,136 @@
 /* bigBedInfo - Show information about a bigBed file.. */
+
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "udc.h"
 #include "bPlusTree.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 #include "obscure.h"
 #include "hmmstats.h"
 
 
 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"
   "   -zooms - list all zoom levels and their sizes\n"
   "   -as - get autoSql spec\n"
   "   -extraIndex - list all the extra indexes\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"udcDir", OPTION_STRING},
    {"chroms", OPTION_BOOLEAN},
    {"zooms", OPTION_BOOLEAN},
    {"as", OPTION_BOOLEAN},
    {"extraIndex", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void printLabelAndLongNumber(char *label, long long l)
 /* Print label: 1,234,567 format number */
 {
 printf("%s: ", label);
 printLongWithCommas(stdout, l);
 printf("\n");
 }
 
 void bigBedInfo(char *fileName)
 /* bigBedInfo - Show information about a bigBed file.. */
 {
 struct bbiFile *bbi = bigBedFileOpen(fileName);
 printf("version: %d\n", bbi->version);
 printf("hasHeaderExtension: %s\n", (bbi->extensionOffset != 0 ? "yes" : "no"));
 printf("isCompressed: %s\n", (bbi->uncompressBufSize > 0 ? "yes" : "no"));
 printf("isSwapped: %d\n", bbi->isSwapped);
 printf("extraIndexCount: %d\n", bbi->extraIndexCount);
 if (optionExists("extraIndex"))
     {
     struct slName *el, *list = bigBedListExtraIndexes(bbi);
     for (el = list; el != NULL; el = el->next)
 	{
 	int fieldIx = 0;
 	struct bptFile *bpt = bigBedOpenExtraIndex(bbi, el->name, &fieldIx);
         printf("    %s (field %d) with %lld items\n", el->name, fieldIx, (long long)bpt->itemCount);
 	}
     }
 printLabelAndLongNumber("itemCount", bigBedItemCount(bbi));
 printLabelAndLongNumber("primaryDataSize", bbi->unzoomedIndexOffset - bbi->unzoomedDataOffset);
 if (bbi->levelList != NULL)
     {
     long long indexEnd = bbi->levelList->dataOffset;
     printLabelAndLongNumber("primaryIndexSize", indexEnd - bbi->unzoomedIndexOffset);
     }
 struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
 printf("zoomLevels: %d\n", bbi->zoomLevels);
 if (optionExists("zooms"))
     {
     struct bbiZoomLevel *zoom;
     for (zoom = bbi->levelList; zoom != NULL; zoom = zoom->next)
 	{
 	printf("\t%d\t%d\n", zoom->reductionLevel, (int)(zoom->indexOffset - zoom->dataOffset));
 	for (chrom=chromList; chrom != NULL; chrom = chrom->next)
 	    {
 	    struct bbiSummary *sum, *sumList = bbiSummariesInRegion(zoom, bbi,   chrom->id,0, chrom->size);
 	     for (sum = sumList; sum != NULL; sum = sum->next)
 	             {
 		     printf("\t\t%s:%d-%d\n",chrom->name, sum->start, sum->end);
 		     }
 				       
 	    }
 
 	}
     }
 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);
 printLabelAndLongNumber("basesCovered", sum.validCount);
 double meanDepth = 0, depthStd = 0;
 if (sum.validCount > 0)
     {
     meanDepth = sum.sumData/sum.validCount;
     depthStd = calcStdFromSums(sum.sumData, sum.sumSquares, sum.validCount);
     }
 printf("meanDepth (of bases covered): %f\n", meanDepth);
 printf("minDepth: %f\n", sum.minVal);
 printf("maxDepth: %f\n", sum.maxVal);
 printf("std of depth: %f\n", depthStd);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 bigBedInfo(argv[1]);
 if (verboseLevel() > 1)
     printVmPeak();
 return 0;
 }