src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c 1.1

Index: src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c
===================================================================
RCS file: src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c
diff -N src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c	24 May 2010 18:09:14 -0000	1.1
@@ -0,0 +1,112 @@
+/* wigSetSpanOrStep - Set span or step variables in an ascii format wiggle file. */
+#include "common.h"
+#include "linefile.h"
+#include "hash.h"
+#include "options.h"
+
+static char const rcsid[] = "$Id$";
+
+boolean gotStep = FALSE;
+boolean gotSpan = FALSE;
+int step = 1;
+int span = 1;
+
+void usage()
+/* Explain usage and exit. */
+{
+errAbort(
+  "wigSetSpanOrStep - Set span or step variables in an ascii format wiggle file\n"
+  "usage:\n"
+  "   wigSetSpanOrStep input.wig output.wig\n"
+  "options:\n"
+  "   -span=N set span variable to given value\n"
+  "   -step=N set step variable to given value\n"
+  "either step or span should be used\n"
+  );
+}
+
+static struct optionSpec options[] = {
+   {"step", OPTION_INT},
+   {"span", OPTION_INT},
+   {NULL, 0},
+};
+
+static void handleStepLine(struct lineFile *lf, char *line, int firstWordSize,
+	boolean isVarStep, FILE *f)
+/* Handle a line that starts with fixedStep or variableStep */
+{
+char *firstPair = skipLeadingSpaces(line + firstWordSize);
+mustWrite(f, line, firstWordSize);
+struct slPair *pair, *pairList = slPairFromString(firstPair);
+boolean seenStep = FALSE, seenSpan = FALSE;
+for (pair = pairList; pair != NULL; pair = pair->next)
+    {
+    if (gotStep && sameString(pair->name, "step"))
+        {
+	fprintf(f, " step=%d", step);
+	seenStep = TRUE;
+	}
+    else if (gotSpan && sameString(pair->name, "span"))
+        {
+	fprintf(f, " span=%d", span);
+	seenSpan = TRUE;
+	}
+    else
+        {
+	fprintf(f, " %s=%s", pair->name, (char *)pair->val);
+	}
+    }
+if (gotStep && !seenStep)
+    {
+    if (isVarStep)
+        errAbort("%s isn't fixed step line %d, can't set step", lf->fileName, lf->lineIx);
+    fprintf(f, " step=%d", step);
+    }
+if (gotSpan && !seenSpan)
+    fprintf(f, " span=%d", span);
+fprintf(f, "\n");
+}
+
+void wigSetSpanOrStep(char *input, char *output)
+/* wigSetSpanOrStep - Set span or step variables in an ascii format wiggle file. */
+{
+struct lineFile *lf = lineFileOpen(input, TRUE);
+FILE *f = mustOpen(output, "w");
+char *line;
+int lineSize;
+char *fixedPat = "fixedStep";
+int fixedPatSize = strlen(fixedPat);
+char *varPat = "variableStep";
+int varPatSize = strlen(varPat);
+while (lineFileNext(lf, &line, &lineSize))
+    {
+    if (startsWithWord(fixedPat, line))
+	handleStepLine(lf, line, fixedPatSize, FALSE, f);
+    else if (startsWithWord(varPat, line))
+	handleStepLine(lf, line, varPatSize, TRUE, f);
+    else
+	{
+        mustWrite(f, line, lineSize-1);
+	fputc('\n', f);
+	}
+    }
+carefulClose(&f);
+}
+
+int main(int argc, char *argv[])
+/* Process command line. */
+{
+optionInit(&argc, argv, options);
+if (argc != 3)
+    usage();
+step = optionInt("step", 0);
+span = optionInt("span", 0);
+if (step != 0)
+    gotStep = TRUE;
+if (span != 0)
+    gotSpan = TRUE;
+if (!step && !span)
+    usage();
+wigSetSpanOrStep(argv[1], argv[2]);
+return 0;
+}