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/ratStuff/multizzy/multizzy.c src/hg/ratStuff/multizzy/multizzy.c
index ac6ffc6..8b217be 100644
--- src/hg/ratStuff/multizzy/multizzy.c
+++ src/hg/ratStuff/multizzy/multizzy.c
@@ -1,112 +1,112 @@
 /* multizzy - Run a lot of multiz jobs. */
 
 /* 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 "portable.h"
 #include "obscure.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "multizzy - Run a lot of multiz jobs\n"
   "usage:\n"
   "   multizzy dirList scaffoldList destDir\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void oneMultiz(char *a, char *b, char *out) 
 /* Call multiz if files exist, otherwise just copy. */
 {
 char command[3*PATH_LEN];
 boolean aExists = fileExists(a);
 boolean bExists = fileExists(b);
 int ret;
 if (aExists && bExists)
     {
     safef(command, sizeof(command), "%s %s %s - > %s", 
     	"multiz", a, b, out);
     ret = system(command);
     if (ret != 0)
         errAbort("%s failed status %d", command, ret);
     }
 else if (aExists)
     {
     copyFile(a, out);
     }
 else if (bExists)
     {
     copyFile(b, out);
     }
 }
 
 void multizzy(char *dirList, char *scaffoldList, char *destDir)
 /* multizzy - Run a lot of multiz jobs. */
 {
 char *dirBuf, *scaffoldBuf;
 int dirCount, scaffoldCount;
 char **dirs, **scaffolds, *dir, *scaffold;
 char command[512];
 int dirIx, scaffoldIx;
 char *tempNames[2];
 
 makeDir(destDir);
 tempNames[0] = "multizzy0.tmp";
 tempNames[1] = "multizzy1.tmp";
 
 readAllWords(dirList, &dirs, &dirCount, &dirBuf);
 readAllWords(scaffoldList, &scaffolds, &scaffoldCount, &scaffoldBuf);
 if (dirCount < 2)
    errAbort("Need at least 2 directories for multizzy to work."); 
 for (scaffoldIx=0; scaffoldIx < scaffoldCount; ++scaffoldIx)
     {
     char *scaffold = scaffolds[scaffoldIx];
     char firstPath[PATH_LEN];
     char destPath[PATH_LEN];
     int flipper = 0;	/* FLip between 1 and 0. */
     verbose(1, "%s\n", scaffold);
     safef(firstPath, sizeof(firstPath), "%s/%s.maf", dirs[0], scaffold);
     safef(destPath, sizeof(destPath), "%s/%s.maf", destDir, scaffold);
     remove(tempNames[0]);
     remove(tempNames[1]);
     for (dirIx=1; dirIx < dirCount; ++dirIx)
         {
 	char path[PATH_LEN];
 	char *mid, *out;
 	if (dirIx == 1)
 	    mid = firstPath;
 	else
 	    mid = tempNames[flipper];
 	if (dirIx == dirCount-1)
 	    out = destPath;
 	else
 	    out = tempNames[1-flipper];
 	safef(path, sizeof(path), "%s/%s.maf", dirs[dirIx], scaffold);
 	oneMultiz(path, mid, out);
 	flipper = 1 - flipper;
 	}
     }
 remove(tempNames[0]);
 remove(tempNames[1]);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 multizzy(argv[1], argv[2], argv[3]);
 return 0;
 }