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/mouseStuff/knownVsBlat/blatStats.c src/hg/mouseStuff/knownVsBlat/blatStats.c
index c45cc66..0002db7 100644
--- src/hg/mouseStuff/knownVsBlat/blatStats.c
+++ src/hg/mouseStuff/knownVsBlat/blatStats.c
@@ -1,159 +1,159 @@
 /* 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 "blatStats.h"
 
 
 
 float divAsPercent(double a, double b)
 /* Return a/b * 100. */
 {
 if (b == 0)
    return 0.0;
 return 100.0 * a / b;
 }
 
 void reportStat(FILE *f, char *name, struct oneStat *stat, boolean reportPercentId)
 /* Print out one set of stats. */
 {
 char buf[64];
 fprintf(f, "%-15s ", name);
 sprintf(buf, "%4.1f%% (%d/%d)", 
 	divAsPercent(stat->basesPainted, stat->basesTotal),
 	stat->basesPainted, stat->basesTotal);
 fprintf(f, "%-25s ", buf);
 sprintf(buf, "%4.1f%% (%d/%d)", 
 	divAsPercent(stat->hits, stat->features),
 	stat->hits, stat->features);
 fprintf(f, "%-20s ", buf);
 if (reportPercentId)
     fprintf(f, "%4.1f%%", divAsPercent(stat->cumIdRatio, stat->basesPainted));
 fprintf(f, "\n");
 }
 
 struct oneStat *totalUtr(struct blatStats *stats)
 /* Return sum of 5' and 3' UTRs. */
 {
 static struct oneStat acc;
 ZeroVar(&acc);
 addStat(&stats->utr5, &acc);
 addStat(&stats->utr3, &acc);
 return &acc;
 }
 
 struct oneStat *totalSplice(struct blatStats *stats)
 /* Return sum of 5' and 3' splice sites. */
 {
 static struct oneStat acc;
 ZeroVar(&acc);
 addStat(&stats->splice5, &acc);
 addStat(&stats->splice3, &acc);
 return &acc;
 }
 
 struct oneStat *totalCds(struct blatStats *stats)
 /* Return sum of all CDS regions. */
 {
 static struct oneStat acc;
 ZeroVar(&acc);
 addStat(&stats->firstCds, &acc);
 addStat(&stats->middleCds, &acc);
 addStat(&stats->endCds, &acc);
 addStat(&stats->onlyCds, &acc);
 return &acc;
 }
 
 struct oneStat *totalIntron(struct blatStats *stats)
 /* Return sum of all intron regions. */
 {
 static struct oneStat acc;
 ZeroVar(&acc);
 addStat(&stats->firstIntron, &acc);
 addStat(&stats->middleIntron, &acc);
 addStat(&stats->endIntron, &acc);
 addStat(&stats->onlyIntron, &acc);
 return &acc;
 }
 
 
 void reportStats(FILE *f, struct blatStats *stats, char *name, boolean reportPercentId)
 /* Print out stats. */
 {
 fprintf(f, "%s stats:\n", name);
 fprintf(f, "region         bases hit           features hit ");
 if (reportPercentId)
     fprintf(f, "percent identity");
 fprintf(f, "\n");
 fprintf(f, "------------------------------------------------");
 if (reportPercentId)
     fprintf(f, "---------------------");
 fprintf(f, "\n");
 reportStat(f, "upstream 100", &stats->upstream100, reportPercentId);
 reportStat(f, "upstream 200", &stats->upstream200, reportPercentId);
 reportStat(f, "upstream 400", &stats->upstream400, reportPercentId);
 reportStat(f, "upstream 800", &stats->upstream800, reportPercentId);
 reportStat(f, "downstream 200", &stats->downstream200, reportPercentId);
 reportStat(f, "mrna total", &stats->mrnaTotal, reportPercentId);
 reportStat(f, "UTR", totalUtr(stats), reportPercentId);
 reportStat(f, "5' UTR", &stats->utr5, reportPercentId);
 reportStat(f, "3' UTR", &stats->utr3, reportPercentId);
 reportStat(f, "CDS", totalCds(stats), reportPercentId);
 reportStat(f, "first CDS", &stats->firstCds, reportPercentId);
 reportStat(f, "middle CDS", &stats->middleCds, reportPercentId);
 reportStat(f, "end CDS", &stats->endCds, reportPercentId);
 reportStat(f, "only CDS", &stats->onlyCds, reportPercentId);
 reportStat(f, "splice", totalSplice(stats), reportPercentId);
 reportStat(f, "5' splice", &stats->splice5, reportPercentId);
 reportStat(f, "3' splice", &stats->splice3, reportPercentId);
 reportStat(f, "intron", totalIntron(stats), reportPercentId);
 reportStat(f, "first intron", &stats->firstIntron, reportPercentId);
 reportStat(f, "middle intron", &stats->middleIntron, reportPercentId);
 reportStat(f, "end intron", &stats->endIntron, reportPercentId);
 reportStat(f, "only intron", &stats->onlyIntron, reportPercentId);
 fprintf(f, "\n");
 }
 
 void addStat(struct oneStat *a, struct oneStat *acc)
 /* Add stat from a into acc. */
 {
 acc->features += a->features;
 acc->hits += a->hits;
 acc->basesTotal += a->basesTotal;
 acc->basesPainted += a->basesPainted;
 acc->cumIdRatio += a->cumIdRatio;
 }
 
 void addStats(struct blatStats *a, struct blatStats *acc)
 /* Add stats in a to acc. */
 {
 addStat(&a->upstream100, &acc->upstream100);
 addStat(&a->upstream200, &acc->upstream200);
 addStat(&a->upstream400, &acc->upstream400);
 addStat(&a->upstream800, &acc->upstream800);
 addStat(&a->mrnaTotal, &acc->mrnaTotal);
 addStat(&a->utr5, &acc->utr5);
 addStat(&a->firstCds, &acc->firstCds);
 addStat(&a->firstIntron, &acc->firstIntron);
 addStat(&a->middleCds, &acc->middleCds);
 addStat(&a->onlyCds, &acc->onlyCds);
 addStat(&a->middleIntron, &acc->middleIntron);
 addStat(&a->onlyIntron, &acc->onlyIntron);
 addStat(&a->endCds, &acc->endCds);
 addStat(&a->endIntron, &acc->endIntron);
 addStat(&a->utr3, &acc->utr3);
 addStat(&a->splice5, &acc->splice5);
 addStat(&a->splice3, &acc->splice3);
 addStat(&a->downstream200, &acc->downstream200);
 }
 
 struct blatStats *sumStatsList(struct blatStats *list)
 /* Return sum of all stats. */
 {
 struct blatStats *el, *stats;
 AllocVar(stats);
 for (el = list; el != NULL; el = el->next)
     addStats(el, stats);
 return stats;
 }