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/makeDb/outside/samHit/samHit.c src/hg/makeDb/outside/samHit/samHit.c
index fe121a7..2f3acd2 100644
--- src/hg/makeDb/outside/samHit/samHit.c
+++ src/hg/makeDb/outside/samHit/samHit.c
@@ -1,118 +1,118 @@
 /* samHit reads the SAM output file, XXXX.t2k.best-scores.rdb and produce .tab data for the protHomolog table */
 
 /* Copyright (C) 2009 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"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "samHit - reads the SAM output .rdb file and produce .tab data for the protHomolog table. "
   "usage:\n"
   "      samHit proteinId rdbFN\n"
   "      proteinId is the protein ID\n"
   "      rdbFN is the .rdb file name\n"
   "      ro_db is the target genome to read data from\n"
   "example:\n"
   "   samHit YNL100W /projects/compbio/experiments/protein-predict/yeast/YNL1/YNL100W.t2k.best-scores.rdb\n");
 }
 
 char *word[10];
 char *previousWord[10];
 char *proteinId;
 
 char getChain(char *id)
 /* parse out the last letter (if it is in upper case) as the Chain  */
     {
     int l;
     char ch, *chp;
     l=strlen(id);
     chp = id+l-1;
     if (isupper(*chp))
     	{
 	ch = *chp;
 	*chp = '\0';
 	return(ch);
 	}
     else
         {
 	return('-');
 	}
     }
 
 void processOneLine(char *line)
 /* process one line */
 {
 int i;
 char *chp;
 char ch;
 
 chp = line;
 for (i=0; i<7; i++)
     {
     word[i] = chp;
     chp = strstr(chp, "\t");
     if (chp != NULL) 
     	{
 	*chp = '\0';
     	chp++;
 	}
     }
 
 for (i=0; i<7; i++)
     {
     if (sameWord(word[i],""))
     	{
 	/* for fields that are empty, use previous ones */
 	word[i] = previousWord[i];
 	}
     previousWord[i] = strdup(word[i]);
     }
 
 ch = getChain(word[0]);
 
 if (ch == '-')
     {
     printf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", proteinId, word[0], "", word[1], word[2], word[3],
 	   word[4], word[5], word[6]);
     }
 else
     {
     printf("%s\t%s\t%c\t%s\t%s\t%s\t%s\t%s\t%s\n", proteinId, word[0], ch, word[1], word[2], word[3],
 	   word[4], word[5], word[6]);
     }
 
 }
 
 int main(int argc, char *argv[])
 {
 FILE *inf;
 char line[1000];
 
 int i;
 char *infileName;
 
 if (argc != 3) usage();
 
 proteinId  = argv[1];
 infileName = argv[2];
 
 for (i=0; i<8; i++) previousWord[i] = strdup("n/a");
     
 inf   = mustOpen(infileName, "r");
 
 /* skip initial 2 header lines in .rdb format file */
 mustGetLine(inf, line, sizeof(line));
 mustGetLine(inf, line, sizeof(line));
 
 /* read and process all lines one by one */
 while (fgets(line, sizeof(line), inf) != NULL)
     {
     *(line + strlen(line) - 1) = '\0';
     processOneLine(line);
     }
 
 return(0);
 }