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/protein/hmmPfamToTab/hmmPfamToTab.c src/hg/protein/hmmPfamToTab/hmmPfamToTab.c
index 6af3e9d..0132c59 100644
--- src/hg/protein/hmmPfamToTab/hmmPfamToTab.c
+++ src/hg/protein/hmmPfamToTab/hmmPfamToTab.c
@@ -1,78 +1,78 @@
 /* hmmPfamToTab - Convert hmmPfam output to something simple and tab-delimited.. */
 
 /* 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 "hash.h"
 #include "options.h"
 #include "hmmPfamParse.h"
 
 
 double eVal = 0.0001;
 boolean eValCol = FALSE;
 boolean scoreCol = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hmmPfamToTab - Convert hmmPfam output to something simple and tab-delimited.\n"
   "usage:\n"
   "   hmmPfamToTab inFile out.tab\n"
   "options:\n"
   "   -eVal=0.N - Set eVal threshold. Default %g\n"
   "   -eValCol  - Include eVal in output\n"
   , eVal
   );
 }
 
 static struct optionSpec options[] = {
    {"eVal", OPTION_DOUBLE},
    {"eValCol", OPTION_BOOLEAN},
    {"scoreCol", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void hmmPfamToTab(char *inFile, char *outFile)
 /* hmmPfamToTab - Convert hmmPfam output to something simple and tab-delimited.. */
 {
 struct lineFile *lf = lineFileOpen(inFile, TRUE);
 FILE *f = mustOpen(outFile, "w");
 struct hpfResult *hr;
 while ((hr = hpfNext(lf)) != NULL)
      {
      struct hpfModel *mod;
      for (mod = hr->modelList; mod != NULL; mod = mod->next)
          {
 	 struct hpfDomain *dom;
 	 for (dom = mod->domainList; dom != NULL; dom = dom->next)
 	     {
 	     if (dom->eVal <= eVal)
 		 {
 		 fprintf(f, "%s\t%d\t%d\t%s", hr->name, dom->qStart, dom->qEnd, mod->name);
 		 if (eValCol)
 		     fprintf(f, "\t%g", dom->eVal);
 		 if (scoreCol)
 		     fprintf(f, "\t%g", dom->score);
 		 fprintf(f, "\n");
 		 }
 	     }
 	 }
      hpfResultFree(&hr);
      }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 eVal = optionDouble("eVal", eVal);
 eValCol = optionExists("eValCol");
 scoreCol = optionExists("scoreCol");
 hmmPfamToTab(argv[1], argv[2]);
 return 0;
 }