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/hgPhMouse/hgPhMouse.c src/hg/makeDb/outside/hgPhMouse/hgPhMouse.c
index 70f5329..4721c38 100644
--- src/hg/makeDb/outside/hgPhMouse/hgPhMouse.c
+++ src/hg/makeDb/outside/hgPhMouse/hgPhMouse.c
@@ -1,132 +1,132 @@
 /* hgPhMouse - Load phMouse track. */
 
 /* 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 "dystring.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "hdb.h"
 #include "bed.h"
 #include "jksql.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgPhMouse - Load phMouse track\n"
   "usage:\n"
   "   hgPhMouse database track chromFile(s)\n"
   "options:\n"
   "   -add - add data, don't overwrite old track\n"
   );
 }
 
 char *createString = 
 "CREATE TABLE %s (\n"
 "    bin smallint unsigned not null,    # Bin index field\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,	# Name of item\n"
 "    score int unsigned not null,	# Score from 0-1000\n"
 "    strand char(1) not null,	# + or -\n"
 "              #Indices\n"
 "    INDEX(chrom(8),bin),\n"
 "    INDEX(chrom(8),chromStart),\n"
 "    INDEX(chrom(8),chromEnd)\n"
 ")\n";
 
 void loadDatabase(char *database, char *track, char *tabName)
 /* Load up database from tab-file. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 struct dyString *dy = newDyString(1024);
 
 
 if (!cgiBoolean("add"))
     {
     sqlDyStringPrintf(dy, createString, track);
     sqlRemakeTable(conn, track, dy->string);
     dyStringClear(dy);
     }
 sqlDyStringPrintf(dy, "load data local infile '%s' into table %s",
 	tabName, track);
 sqlUpdate(conn, dy->string);
 dyStringFree(&dy);
 sqlDisconnect(&conn);
 }
 
 
 void hgPhMouse(char *database, char *track, int fileCount, char *fileNames[])
 /* hgPhMouse - Load phMouse track. */
 {
 int i;
 char *fileName;
 char *tabName = "phMouse.tab";
 FILE *f = mustOpen(tabName, "w");
 struct lineFile *lf;
 char *words[32], *s, c;
 int wordCount;
 int oneSize, totalSize = 0;
 
 for (i=0; i<fileCount; ++i)
     {
     struct bed *bedList = NULL, *bed;
     fileName = fileNames[i];
     lf = lineFileOpen(fileName, TRUE);
     printf("Reading %s ", fileName);
     fflush(stdout);
     while ((wordCount = lineFileChop(lf, words)) > 0)
         {
 	if (wordCount < 7)
 	   errAbort("Expecting at least 7 words line %d of %s", 
 	   	lf->lineIx, fileName);
 	AllocVar(bed);
 	bed->chrom = cloneString(words[0]);
 	bed->chromStart = lineFileNeedNum(lf, words, 1);
 	bed->chromEnd = lineFileNeedNum(lf, words, 2);
 	bed->score = lineFileNeedNum(lf, words, 6);
 	s = strrchr(words[3], '|');
 	c = s[1];
 	s[0] = 0;
 	if (c != '+' && c != '-')
 	    errAbort("Misformed strandless trace name line %d of %s",
 	    	lf->lineIx, lf->fileName);
 	bed->name = cloneString(words[3]);
 	bed->strand[0] = c;
 	slAddHead(&bedList, bed);
 	}
     oneSize = slCount(bedList);
     printf("%d alignments ", oneSize);
     totalSize += oneSize;
     fflush(stdout);
     slSort(&bedList, bedCmp);
     printf("sorted ");
     fflush(stdout);
     for (bed = bedList; bed != NULL; bed = bed->next)
         {
 	int bin = hFindBin(bed->chromStart, bed->chromEnd);
 	fprintf(f, "%d\t", bin);
 	bedTabOutN(bed, 6, f);
 	}
     printf("tabbed out\n");
     bedFreeList(&bedList);
     }
 carefulClose(&f);
 printf("Loading %d items into %s.%s\n", totalSize, database, track);
 loadDatabase(database, track, tabName);
 remove(tabName);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc < 4)
     usage();
 hgPhMouse(argv[1], argv[2], argc-3, argv+3);
 return 0;
 }