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/borfBig/borfBig.c src/hg/borfBig/borfBig.c
index ac3d2af..6df8157 100644
--- src/hg/borfBig/borfBig.c
+++ src/hg/borfBig/borfBig.c
@@ -1,127 +1,127 @@
 /* borfBig - Run Victor Solovyev's bestorf repeatedly. */
 
 /* 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 "fa.h"
 #include "dystring.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "borfBig - Run Victor Solovyev's bestorf repeatedly\n"
   "usage:\n"
   "   borfBig in.fa out.tab\n"
   "options:\n"
   "   -exe=borf - where exe file belongs\n"
   "   -tmpFa=file - where to put temp .fa file\n"
   "   -tmpOrf=file - where to put temp bestorf output file\n"
   );
 }
 
 char *mustFindLine(struct lineFile *lf, char *pat)
 /* Find line that starts (after skipping white space)
  * with pattern or die trying.  Skip over pat in return*/
 {
 char *line;
 while (lineFileNext(lf, &line, NULL))
     {
     line = skipLeadingSpaces(line);
     if (startsWith(pat, line))
 	{
 	line += strlen(pat);
 	return skipLeadingSpaces(line);
 	}
     }
 errAbort("Couldn't find %s in %s\n", pat, lf->fileName);
 return NULL;
 }
 
 void convertBorfOutput(char *fileName, FILE *f)
 /* Convert bestorf output to our database format. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line = mustFindLine(lf, "BESTORF");
 char *word;
 char *row[13];
 struct dnaSeq seq;
 int seqSize;
 ZeroVar(&seq);
 
 line = mustFindLine(lf, "Seq name:");
 word = nextWord(&line);
 fprintf(f, "%s\t", word);                            /* Name */
 line = mustFindLine(lf, "Length of sequence:");
 seqSize = atoi(line);                                /* Size */
 fprintf(f, "%d\t", seqSize);
 lineFileNeedNext(lf, &line, NULL);
 line = skipLeadingSpaces(line);
 if (startsWith("no reliable", line))
     {
     fprintf(f, ".\tn/a\t0\t0\t0.0\t0\t0\t0\t0\t\n");
     }
 else
     {
     line = mustFindLine(lf, "G Str F");
     lineFileSkip(lf, 1);
     lineFileRow(lf, row);
 
     fprintf(f, "%s\t", row[1]);                          /* Strand */
     fprintf(f, "%s\t", row[3]);                          /* Feature */
     fprintf(f, "%d\t", lineFileNeedNum(lf, row, 4) - 1); /* cdsStart */
     fprintf(f, "%d\t", lineFileNeedNum(lf, row, 6));     /* cdsEnd */
     fprintf(f, "%s\t", row[7]);                          /* score */
     fprintf(f, "%d\t", lineFileNeedNum(lf, row, 8) - 1); /* orfStart */
     fprintf(f, "%d\t", lineFileNeedNum(lf, row, 10));    /* orfEnd */
     fprintf(f, "%s\t", row[11]);                         /* cdsSize */
     fprintf(f, "%s\t", row[12]);                         /* frame */
     line = mustFindLine(lf, "Predicted protein");
     if (!faPepSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
 	errAbort("Can't find peptide in %s", lf->fileName);
     fprintf(f, "%s\n", seq.dna);
     }
 lineFileClose(&lf);
 }
 
 void borfBig(char *inName, char *outName)
 /* borfBig - Run Victor Solovyev's bestorf repeatedly. */
 {
 char *exe = optionVal("exe", "borf");
 char *tmpFa = optionVal("tmpFa", cloneString(rTempName("/tmp", "borf", ".fa")));
 char *tmpOrf = optionVal("tmpOrf", cloneString(rTempName("/tmp", "borf", ".out")));
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 FILE *f = mustOpen(outName, "w");
 struct dnaSeq seq;
 struct dyString *cmd = newDyString(256);
 ZeroVar(&seq);
 
 while (faSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
     {
     faWrite(tmpFa, seq.name, seq.dna, seq.size);
     dyStringClear(cmd);
     dyStringPrintf(cmd, "%s %s > %s", exe, tmpFa, tmpOrf);
     mustSystem(cmd->string);
     convertBorfOutput(tmpOrf, f);
     printf(".");
     fflush(stdout);
     }
 printf("\n");
 remove(tmpFa);
 remove(tmpOrf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc != 3)
     usage();
 borfBig(argv[1], argv[2]);
 return 0;
 }