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/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
index d2f0dc8..e21b201 100644
--- src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
+++ src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
@@ -1,141 +1,141 @@
 /* wgEncodeRegGenRa - Help generate some of the wgEncodeReg.ra file.. */
 
 /* 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 "options.h"
 #include "jksql.h"
 #include "bigWig.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "wgEncodeRegGenRa - Help generate some of the wgEncodeReg.ra file.\n"
   "usage:\n"
   "   wgEncodeRegGenRa now\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 struct markInfo
 /* Info on a histone mark or the like. */
     {
     char *part;		/* Part as used in file and track names */
     char *name;		/* Human readable name */
     char *blurb;	/* Short description */
     char *vis;		/* Visibility */
     int yMax;		/* Top before clipping */
     };
 
 
 struct markInfo marks[] = {
     { "H3k4me1", "H3K4Me1", "Often Found Near Regulatory Elements", "full", 150},
     { "H3k4me3", "H3K4Me3", "Often Found Near Promoters", "full", 250},
     { "H3k9ac", "H3K9Ac", "Often Found Near Regulatory Elements", "hide", 200},
     { "H3k27ac", "H3K27Ac", "Often Found Near Regulatory Elements", "hide", 200},
     { "H3k27me3", "H3K27Me3", "Polycomb silenced", "hide", 150},
     { "H3k36me3", "H3K36Me3", "Marks Areas of RNA PolII Elongation", "hide", 100},
     { "H4k20me1", "H3K30Me1", "Associated with Active Accessible Regions", "hide", 150},
     { "Ctcf", "CTCF", "Insulator/DNA Looping", "hide", 300},
     { "Control", "Input Control", "Input Control - used to filter peaks", "hide", 150},
 };
 
 struct cellInfo
 /* Info on a cell line */
     {
     char *part;		/* Part as used in file and track names */
     char *name;		/* Human readable name */
     int r,g,b;		/* Color */
     };
 
 struct cellInfo cells[] = {
     { "Gm12878", "GM12878", 255,128,128, },
     { "H1hesc", "H1-hESC", 255,212,128, },
     { "Helas3", "HeLa-S3", 227, 255, 128,},
     { "Hepg2", "HepG2", 128,255,149,},
     { "Hsmm", "HSMM", 128,255,242, },
     { "Huvec", "HUVEC", 128,199,255, },
     { "K562", "K562", 149,128,255, },
     { "Nhek", "NHEK", 227,128,255, },
     { "Nhlf", "NHLF", 255,128,212, },
 };
 
 void wgEncodeRegGenRa(char *now)
 /* wgEncodeRegGenRa - Help generate some of the wgEncodeReg.ra file. */
 {
 struct sqlConnection *conn = sqlConnect("hg19");
 int i;
 for (i=0; i<ArraySize(marks); ++i)
     {
     struct markInfo *mark = &marks[i];
     printf("    track wgEncodeRegMarkNorm%s\n", mark->part);
     printf("    container multiWig\n");
     printf("    noInherit on\n");
     printf("    type bigWig 0 10000\n");
     printf("    superTrack wgEncodeReg full\n");
     printf("    shortLabel Normaliz %s\n", mark->name);
     printf("    longLabel %s Normalized (%s) on 9 cell lines from ENCODE\n", mark->name, mark->blurb);
     printf("    visibility %s\n", mark->vis);
     printf("    viewLimits 0:%d\n", mark->yMax);
     printf("    maxHeightPixels 100:50:11\n");
     printf("    aggregate transparentOverlay\n");
     printf("    showSubtrackColorOnUi on\n");
     printf("    priority 2.%d\n", i+2);
     printf("    dragAndDrop subtracks\n");
     printf("\n");
 
     int j;
     for (j=0; j<ArraySize(cells); ++j)
         {
 	struct cellInfo *cell = &cells[j];
 
 	/* Get table, and see if it exists.  If so get info from it. */
 	boolean tableExists = FALSE;
 	int wigMax = 10000;
 	char table[256];
 	safef(table, sizeof(table), "wgEncodeBroadHistone%s%sNormSig", cell->part, mark->part);
 	if (sqlTableExists(conn, table))
 	    {
 	    tableExists = TRUE;
 	    char query[512];
 	    sqlSafef(query, sizeof(query), "select fileName from %s", table);
 	    char *fileName = sqlQuickString(conn, query);
 	    struct bbiFile *bbi = bigWigFileOpen(fileName);
 	    struct bbiSummaryElement sum = bbiTotalSummary(bbi);
 	    wigMax = sum.maxVal;
 	    bbiFileClose(&bbi);
 	    }
 	printf("\ttrack wgEncodeRegMarkNorm%s%s\n", mark->part, cell->part);
 	printf("\ttable %s\n", table);
 	if (!tableExists)
 	    printf("\t#%s table doesn't exist\n", table);
 	printf("\tshortLabel %s\n", cell->name);
 	printf("\tlongLabel %s Normalized (%s) on %s Cells from ENCODE\n",
 		mark->name, mark->blurb, cell->name);
 	printf("\tparent wgEncodeRegMarkNorm%s\n", mark->part);
 	printf("\tcolor %d,%d,%d\n", cell->r, cell->g, cell->b);
 	printf("\ttype bigWig 0 %d\n", wigMax);
 	printf("\n");
 	}
     }
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 wgEncodeRegGenRa(argv[1]);
 return 0;
 }