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/hgLoadWiggle/wigEncode.c src/hg/makeDb/hgLoadWiggle/wigEncode.c
index cbf1682..9348082 100644
--- src/hg/makeDb/hgLoadWiggle/wigEncode.c
+++ src/hg/makeDb/hgLoadWiggle/wigEncode.c
@@ -1,137 +1,137 @@
 /* wigEncode - Convert wiggle ascii to wiggle binary format */
 
 /* 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 "wiggle.h"
 #include "options.h"
 #include "obscure.h"
 
 void usage()
 /* Explain usage and exit */
 {
 errAbort("wigEncode - convert Wiggle ascii data to binary format\n\n"
     "usage:\n"
     "    wigEncode [options] wigInput wigFile wibFile\n"
     "\twigInput - wiggle ascii data input file (stdin OK)\n"
     "\twigFile - .wig output file to be used with hgLoadWiggle\n"
     "\twibFile - .wib output file to be symlinked into /gbdb/<db>/wib/\n"
     "\n"
     "This processes the three data input format types described at:\n"
     "\thttp://genome.ucsc.edu/encode/submission.html#WIG\n"
     "\t(track and browser lines are tolerated, i.e. ignored)\n"
     "options:\n"
     "    -lift=<D> - lift all input coordinates by D amount, default 0\n"
     "              - can be negative as well as positive\n"
     "    -allowOverlap - allow overlapping data, default: overlap not allowed\n"
     "              - only effective for fixedStep and if fixedStep declarations\n"
     "              - are in order by chromName,chromStart\n"
     "    -noOverlapSpanData - check for overlapping span data\n"
     "    -wibSizeLimit=<N> - ignore rest of input when wib size is >= N\n"
     "\n"
     "Example:\n"
     "    hgGcPercent -wigOut -doGaps -file=stdout -win=5 xenTro1 \\\n"
     "        /cluster/data/xenTro1 | "
     "wigEncode stdin gc5Base.wig gc5Base.wib\n"
     "load the resulting .wig file with hgLoadWiggle:\n"
     "    hgLoadWiggle -pathPrefix=/gbdb/xenTro1/wib xenTro1 gc5Base gc5Base.wig\n"
     "    ln -s `pwd`/gc5Base.wib /gbdb/xenTro1/wib"
     );
 }
 
 static struct optionSpec optionSpecs[] = {
     {"lift", OPTION_INT},
     {"noOverlap", OPTION_BOOLEAN},
     {"allowOverlap", OPTION_BOOLEAN},
     {"noOverlapSpanData", OPTION_BOOLEAN},
     {"wibSizeLimit", OPTION_LONG_LONG},
     {NULL, 0}
 };
 
 static int lift = 0;		/*	offset to lift positions on input */
 static boolean noOverlap = TRUE;	/*	check for overlapping data */
 static boolean allowOverlap = FALSE;	/* do not check for overlapping data */
 static boolean noOverlapSpanData = FALSE; /* verify span data doesn't overlap */
 static long long wibSizeLimit = 0;	/*	governor on ct trash sizes */
 
 void wigEncode(char *bedFile, char *wigFile, char *wibFile)
 /* Convert BED file to wiggle binary representation */
 {
 double upper=wigEncodeStartingUpperLimit, lower=wigEncodeStartingLowerLimit;
 if ((lift != 0) || noOverlap || noOverlapSpanData || (wibSizeLimit > 0))
     {
     struct wigEncodeOptions options;
 
     ZeroVar(&options);	/*	make sure everything is zero	*/
     options.lift = lift;
     options.noOverlap = noOverlap;
     options.flagOverlapSpanData = noOverlapSpanData;
     options.wibSizeLimit = wibSizeLimit;
     wigAsciiToBinary(bedFile, wigFile, wibFile, &upper, &lower, &options);
     if ((wibSizeLimit > 0) && (options.wibSizeLimit >= wibSizeLimit))
 	verbose(1,"#\twarning, reached wiggle size limits, %lld vs. %lld\n",
 		wibSizeLimit, options.wibSizeLimit);
     }
 else
     wigAsciiToBinary(bedFile, wigFile, wibFile, &upper, &lower, NULL);
 
 if ( (wigEncodeStartingUpperLimit == upper) &&
 	(wigEncodeStartingLowerLimit == lower) )
     errAbort("ERROR: wigEncode: empty input file: '%s'", bedFile );
 
 verbose(1, "Converted %s, upper limit %.2f, lower limit %.2f\n",
                         bedFile, upper, lower);
 }
 
 int main( int argc, char *argv[] )
 /* Process command line */
 {
 optionInit(&argc, argv, optionSpecs);
 
 lift = optionInt("lift", 0);
 wibSizeLimit = optionLongLong("wibSizeLimit", 0);
 allowOverlap = optionExists("allowOverlap");
 noOverlapSpanData = optionExists("noOverlapSpanData");
 if (wibSizeLimit < 0)	/*	protect against negative limits	*/
     {
     wibSizeLimit = 0;
     verbose(1,"warning: negative wibSizeLimit specified, becomes zero\n");
     }
 
 if (argc < 4)
     usage();
 if (optionExists("noOverlap") && allowOverlap)
     {
     verbose(1,"wigEncode: can not specify -noOverlap and -allowOverlap together\n");
     usage();
     }
 if (optionExists("noOverlap"))
     {
     verbose(1,"warning: -noOverlap is now the default, no need to specify that\n");
     verbose(1,"\tsee also: -allowOverlap\n");
     }
 
 if (lift != 0)
     verbose(2,"option lift=%d to lift all positions by %d\n", lift, lift);
 if (wibSizeLimit > 0)
     verbose(2,"option wibSizeLimit=%lld\n", wibSizeLimit);
 if (noOverlapSpanData)
     {
     verbose(2,"option noOverlapSpanData on, will *not* allow overlapping spanned data\n" );
     }
 if (allowOverlap)
     {
     verbose(2,"option allowOverlap on, will allow overlapping data\n" );
     noOverlap = FALSE;
     }
 verbose(2,"input ascii data file: %s\n", argv[1]);
 verbose(2,"output .wig file: %s\n", argv[2]);
 verbose(2,"output .wib file: %s\n", argv[3]);
 
 wigEncode(argv[1], argv[2], argv[3]);
 if (verboseLevel() > 1)
     printVmPeak();
 exit(0);
 }