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/snp/snpLoad/fetchSeq.c src/hg/snp/snpLoad/fetchSeq.c
index 861bc24..35c1af1 100644
--- src/hg/snp/snpLoad/fetchSeq.c
+++ src/hg/snp/snpLoad/fetchSeq.c
@@ -1,92 +1,92 @@
 /* fetchSeq  */
 /* Input is bed 6. */
 /* Output adds sequence as column 7. */
 /* The key thing here is doing a reverse complement for data on the negative strand. */
 /* Not checking for coords off the end of the chrom. */
 
 /* 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 "dnaseq.h"
 #include "linefile.h"
 #include "sqlNum.h"
 #include "twoBit.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "fetchSeq - append sequence to bed 6\n"
     "usage:\n"
     "    fetchSeq input sequence output\n");
 }
 
 
 void doFetch(char *inputFileName, char *sequenceFileName, char *outputFileName)
 /* lookup sequence for each line */
 {
 struct lineFile *lf = NULL;
 char *line;
 char *row[6];
 int elementCount;
 struct twoBitFile *tbf;
 
 char *fileChrom = NULL;
 int start = 0;
 int end = 0;
 char *name = NULL;
 int score = 0;
 char *strand = NULL;
 
 struct dnaSeq *chunk = NULL;
 
 FILE *outputFileHandle = mustOpen(outputFileName, "w");
 
 tbf = twoBitOpen(sequenceFileName);
 
 lf = lineFileOpen(inputFileName, TRUE);
 while (lineFileNext(lf, &line, NULL))
     {
     elementCount = chopString(line, "\t", row, ArraySize(row));
     if (elementCount != 6) continue;
 
     fileChrom = cloneString(row[0]);
     start = sqlUnsigned(row[1]);
     end = sqlUnsigned(row[2]);
     name = cloneString(row[3]);
     score = sqlUnsigned(row[4]);
     strand = cloneString(row[5]);
 
     if (start == end) continue;
     assert (end > start);
 
     chunk = twoBitReadSeqFrag(tbf, fileChrom, start, end);
     touppers(chunk->dna);
     if (sameString(strand, "-"))
         reverseComplement(chunk->dna, chunk->size);
     fprintf(outputFileHandle, "%s\t%d\t%d\t%s\t%d\t%s\t%s\n", fileChrom, start, end, name, score, strand, chunk->dna);
     dnaSeqFree(&chunk);
     }
 
 lineFileClose(&lf);
 carefulClose(&outputFileHandle);
 }
 
 
 int main(int argc, char *argv[])
 /* read bed 6 file, look up sequence */
 {
 if (argc != 4)
     usage();
 
 if (!fileExists(argv[1]))
     errAbort("can't find %s\n", argv[1]);
 if (!fileExists(argv[2]))
     errAbort("can't find %s\n", argv[2]);
 
 doFetch(argv[1], argv[2], argv[3]);
 
 return 0;
 }