4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/qacToWig/qacToWig.c src/hg/qacToWig/qacToWig.c
index 6533d3f..cec96ae 100644
--- src/hg/qacToWig/qacToWig.c
+++ src/hg/qacToWig/qacToWig.c
@@ -1,124 +1,124 @@
 /* qacToWig - convert from compressed quality score format to wig ASCII. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "qaSeq.h"
 #include "options.h"
 #include "portable.h"
 
 
 static char *name = NULL;
 static bool fixed = FALSE;
 
 static struct optionSpec options[] = {
         {"name", OPTION_STRING},
         {"fixed", OPTION_BOOLEAN},
         {NULL, 0}
 };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
 "qacToWig - convert from compressed quality score format to wiggle format.\n"
 "usage:\n"
 "   qacToWig in.qac outFileOrDir\n"
    "\t-name=name    restrict output to just this sequence name\n"
    "\t-fixed        output single file with wig headers and fixed step size\n"
 "   If neither -name nor -fixed is used, outFileOrDir is a directory which\n"
 "   will be created if it does not already exist.  If -name and/or -fixed is\n"
 "   used, outFileOrDir is a file (or \"stdout\").\n"
     );
 
 }
 
 void wigWrite(char *fileName, struct qaSeq *qa)
 /* write a qa entry in wig format to fileName */
 {
 int i;
 FILE *out = mustOpen(fileName, "wb");
 for (i=0; i < qa->size; i++)
     {
     fprintf(out, "%d %d\n", i+1, qa->qa[i]);
     }
 carefulClose(&out);
 }
 
 void wigFixedWrite(FILE *out , struct qaSeq *qa)
 /* write out a qa entry in fixed wig format */
 {
 int i;
 fprintf(out, "fixedStep chrom=%s start=1 step=1\n", qa->name);
 for (i=0; i < qa->size; i++)
     {
     fprintf(out, "%d\n", qa->qa[i]);
     }
 }
 
 void qacToWig(char *inName, char *outDir)
 /* qacToWig - convert from compressed to wiggle format files in out dir */
 {
 boolean isSwapped;
 FILE *in = qacOpenVerify(inName, &isSwapped);
 FILE *out = NULL;
 struct qaSeq *qa;
 int outFileCount = 0;
 
 if (fixed)
     out = mustOpen(outDir, "wb");
 else if (name == NULL)
     makeDir(outDir);
 
 while ((qa = qacReadNext(in, isSwapped)) != NULL)
     {
     if (name != NULL)
 	{
 	if (sameString(qa->name, name))
 	    {
 	    if (fixed)
 		wigFixedWrite(out, qa);
 	    else
 		wigWrite(outDir, qa);
 	    qaSeqFree(&qa);
 	    outFileCount++;
 	    break;
 	    }
 	}
     else if (fixed)
         {
         wigFixedWrite(out, qa);
 	qaSeqFree(&qa);
         outFileCount = 1;
         continue;
         }
     else
 	{
 	char outPath[1024];
 	safef(outPath, sizeof outPath, "%s/%s.wig", outDir, qa->name);
 	wigWrite(outPath, qa);
 	outFileCount++;
 	}
     qaSeqFree(&qa);
     }
 carefulClose(&in);
 if (fixed)
     carefulClose(&out);
 if (name == NULL)
     verbose(1, "Made %d .wig files in %s\n", outFileCount, outDir);
 else if (outFileCount < 1)
     warn("Found no sequences with name \"%s\"\n", name);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);   
 if (argc < 2)
     usage();
 name = optionVal("name", NULL);
 fixed = optionExists("fixed");
 qacToWig(argv[1], argv[2]);
 return 0;
 }