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bedTools/bigWigToWig.c

+/* bigWigToWig - Convert bigWig to wig.  This will keep more of the same structure of the 
+ * original wig than bigWigToBedGraph does, but still will break up large stepped sections into 
+ * smaller ones. */
+
+/* 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 "udc.h"
+#include "bigWig.h"
+#include "obscure.h"
+
+
+char *clChrom = NULL;
+int clStart = -1;
+int clEnd = -1;
+
+void usage()
+/* Explain usage and exit. */
+{
+errAbort(
+  "bigWigToWig - Convert bigWig to wig.  This will keep more of the same structure of the\n"
+  "original wig than bigWigToBedGraph does, but still will break up large stepped sections\n"
+  "into smaller ones.\n"
+  "usage:\n"
+  "   bigWigToWig in.bigWig out.wig\n"
+  "options:\n"
+  "   -chrom=chr1 - if set restrict output to given chromosome\n"
+  "   -start=N - if set, restrict output to only that over start\n"
+  "   -end=N - if set, restict output to only that under end\n"
+  "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
+  );
+}
+
+static struct optionSpec options[] = {
+   {"chrom", OPTION_STRING},
+   {"start", OPTION_INT},
+   {"end", OPTION_INT},
+   {"udcDir", OPTION_STRING},
+   {NULL, 0},
+};
+
+void bigWigToWig(char *inFile, char *outFile)
+/* bigWigToWig - Convert bigWig to wig.  This will keep more of the same structure of the 
+ * original wig than bigWigToBedGraph does, but still will break up large stepped sections into 
+ * smaller ones. */
+{
+struct bbiFile *bwf = bigWigFileOpen(inFile);
+FILE *f = mustOpen(outFile, "w");
+struct bbiChromInfo *chrom, *chromList = bbiChromList(bwf);
+for (chrom = chromList; chrom != NULL; chrom = chrom->next)
+    {
+    if (clChrom != NULL && !sameString(clChrom, chrom->name))
+        continue;
+    char *chromName = chrom->name;
+    int start = 0, end = chrom->size;
+    if (clStart > 0)
+        start = clStart;
+    if (clEnd > 0)
+        end = clEnd;
+    bigWigIntervalDump(bwf, chromName, start, end, 0, f);
+    }
+bbiChromInfoFreeList(&chromList);
+carefulClose(&f);
+bbiFileClose(&bwf);
+}
+
+int main(int argc, char *argv[])
+/* Process command line. */
+{
+optionInit(&argc, argv, options);
+if (argc != 3)
+    usage();
+clChrom = optionVal("chrom", clChrom);
+clStart = optionInt("start", clStart);
+clEnd = optionInt("end", clEnd);
+udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
+bigWigToWig(argv[1], argv[2]);
+if (verboseLevel() > 1)
+    printVmPeak();
+return 0;
+}