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/oneShot/faFiltMasked/faFiltMasked.c src/hg/oneShot/faFiltMasked/faFiltMasked.c
index 67c9e74..28bbe3d 100644
--- src/hg/oneShot/faFiltMasked/faFiltMasked.c
+++ src/hg/oneShot/faFiltMasked/faFiltMasked.c
@@ -1,76 +1,76 @@
 /* faFiltMasked - Filter out reads that have less than 100 base pairs unmasked. */
 
 /* 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 "dnautil.h"
 #include "fa.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faFiltMasked - Filter out reads that have less than 100 base pairs unmasked\n"
   "usage:\n"
   "   faFiltMasked output.fa inFile(s).fa\n");
 }
 
 int uniqCount(DNA *dna, int size)
 /* Count up  non-N bases. */
 {
 int count = 0;
 int i;
 for (i=0; i<size; ++i)
     if (ntChars[dna[i]] )
         ++count;
 return count;
 }
 
 void faFiltMasked(char *outName, int inCount, char *inNames[])
 /* faFiltMasked - Filter out reads that have less than 100 base pairs unmasked. */
 {
 char *inName;
 FILE *out = mustOpen(outName, "w");
 FILE *in;
 DNA *dna;
 int size;
 char *name;
 int i;
 int allCount = 0, goodCount = 0;
 
 
 for (i=0; i<inCount; ++i)
     {
     inName = inNames[i];
     in = mustOpen(inName, "r");
     while (faFastReadNext(in, &dna, &size, &name))
 	{
 	++allCount;
 	if ((allCount&0x1fff) == 0)
 	    {
 	    printf(".");
 	    fflush(stdout);
 	    }
 	if (uniqCount(dna, size) >= 100)
 	    {
 	    ++goodCount;
 	    faWriteNext(out, name, dna, size);
 	    }
 	}
     fclose(in);
     }
 fclose(out);
 printf("\n");
 printf("Wrote %d of %d sequences to %s\n", goodCount, allCount, outName);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc < 3)
     usage();
 dnaUtilOpen();
 faFiltMasked(argv[1], argc-2, argv+2);
 return 0;
 }