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/hgSoftPromoter/hgSoftPromoter.c src/hg/makeDb/outside/hgSoftPromoter/hgSoftPromoter.c
index d020987..e403d14 100644
--- src/hg/makeDb/outside/hgSoftPromoter/hgSoftPromoter.c
+++ src/hg/makeDb/outside/hgSoftPromoter/hgSoftPromoter.c
@@ -1,133 +1,133 @@
 /* hgSoftPromoter - Slap Softberry promoter file into database.. */
 
 /* Copyright (C) 2013 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 "cheapcgi.h"
 #include "jksql.h"
 #include "softPromoter.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgSoftPromoter - Slap Softberry promoter file into database.\n"
   "usage:\n"
   "   hgSoftPromoter database files(s).prom\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 char createString[] = NOSQLINJ "CREATE TABLE softPromoter (\n"
     "chrom varchar(255) not null,	# Human chromosome or FPC contig\n"
     "chromStart int unsigned not null,	# Start position in chromosome\n"
     "chromEnd int unsigned not null,	# End position in chromosome\n"
     "name varchar(255) not null,	# As displayed in browser\n"
     "score int unsigned not null,	# Score from 0 to 1000\n"
     "type varchar(255) not null,	# TATA+ or TATAless currently\n"
     "origScore float not null,	# Score in original file, not scaled\n"
     "origName varchar(255) not null,	# Name in original file\n"
     "blockString varchar(255) not null,	# From original file.  \n"
               "#Indices\n"
     "INDEX(chrom(12),chromStart),\n"
     "INDEX(chrom(12),chromEnd),\n"
     "INDEX(name(12))\n"
 ")\n";
 
 char *simplifyName(char *softName)
 /* Convert softberry name to something ok to see in browser */
 {
 static char simple[256];
 softName += 3;	/* Skip over 'gn:' */
 if (startsWith("NM_", softName))
     {
     char *e = strchr(softName+3, '_');
     if (e != NULL) 
         *e = 0;
     strncpy(simple, softName, sizeof(simple));
     }
 else if (startsWith("FGENESH+_", softName))
     {
     sprintf(simple, "fgene+%s", softName+9);
     }
 else
     {
     strncpy(simple, softName, sizeof(simple));
     simple[16] = 0;
     }
 return simple;
 }
 
 int milliScore(double score)
 /* Return scaled score. */
 {
 int milli = round(score*500);
 if (milli < 0) milli = 0;
 if (milli > 1000) milli = 1000;
 return milli;
 }
 
 void oneFile(char *fileName, FILE *f)
 /* Parse one input file and add to tab separated output. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char chromName[128];
 char *row[9];
 splitPath(fileName, NULL, chromName, NULL);
 
 printf("Parsing %s\n", fileName);
 while (lineFileRow(lf, row))
     {
     fprintf(f, "%s\t", chromName);
     fprintf(f, "%d\t", lineFileNeedNum(lf, row, 1)-1);
     fprintf(f, "%d\t", lineFileNeedNum(lf, row, 2));
     fprintf(f, "%s\t", simplifyName(row[7]));
     fprintf(f, "%d\t", milliScore(atof(row[6])));
     fprintf(f, "%s\t", row[4]);
     fprintf(f, "%s\t", row[6]);
     fprintf(f, "%s\t", row[7]);
     fprintf(f, "%s\n", row[8]);
     }
 lineFileClose(&lf);
 }
 
 void loadDatabase(char *database, char *fileName)
 /* Load database table from tab-separated file. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 char query[256];
 
 printf("Loading %s from %s\n", database, fileName);
 sqlMaybeMakeTable(conn, "softPromoter", createString);
 sqlUpdate(conn, NOSQLINJ "delete from softPromoter");
 sqlSafef(query, sizeof query, "load data local infile '%s' into table softPromoter", fileName);
 sqlUpdate(conn, query);
 sqlDisconnect(&conn);
 }
 
 void hgSoftPromoter(char *database, int fileCount, char *fileNames[])
 /* hgSoftPromoter - Slap Softberry promoter file into database.. */
 {
 char *tabFile = "softPromoter.tab";
 FILE *f = mustOpen(tabFile, "w");
 int i;
 
 for (i=0; i<fileCount; ++i)
     oneFile(fileNames[i], f);
 carefulClose(&f);
 loadDatabase(database, tabFile);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc <= 3)
     usage();
 hgSoftPromoter(argv[1], argc-2, argv+2);
 return 0;
 }