more programs

bedTools/.gitignore

@@ -3,15 +3,17 @@ libs/old
 
 *.o
 *.tar.gz
+*_static
 
 bedGraphToBigWig
 bedToBigBed
-wigToBedGraph
+bigBedInfo
+bigBedSummary
+bigBedToBed
+bigWigInfo
+bigWigSummary
+bigWigToBedGraph
+bigWigToWig
 wigToBed
+wigToBedGraph
 wigToBigWig
-
-bedGraphToBigWig_static
-bedToBigBed_static
-wigToBedGraph_static
-wigToBed_static
-wigToBigWig_static

bedTools/bigBedInfo.c

+/* 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("fieldCount: %d\n", bbi->fieldCount);
+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;
+}

bedTools/bigBedSummary.c

+/* bigBedSummary - Extract summary information from a bigBed file.. */
+
+/* Copyright (C) 2011 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 "sqlNum.h"
+#include "bigBed.h"
+#include "asParse.h"
+#include "udc.h"
+#include "obscure.h"
+
+
+char *summaryType = "coverage";
+
+void usage()
+/* Explain usage and exit. */
+{
+errAbort(
+  "bigBedSummary - Extract summary information from a bigBed file.\n"
+  "usage:\n"
+  "   bigBedSummary 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"
+  "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
+  );
+}
+
+static struct optionSpec options[] = {
+   {"type", OPTION_STRING},
+   {"fields", OPTION_BOOLEAN},
+   {"udcDir", OPTION_STRING},
+   {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 = strtod("NaN", NULL);
+double summaryValues[dataPoints];
+int i;
+for (i=0; i<dataPoints; ++i)
+    summaryValues[i] = nan0;
+
+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);
+udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
+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]));
+    }
+if (verboseLevel() > 1)
+    printVmPeak();
+return 0;
+}