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/tetDensity/tetDensity.c src/hg/oneShot/tetDensity/tetDensity.c
index a0438e9..22a39e6 100644
--- src/hg/oneShot/tetDensity/tetDensity.c
+++ src/hg/oneShot/tetDensity/tetDensity.c
@@ -1,132 +1,132 @@
 /* tetDensity - density of tetraodon alignments vs. chromosomes. */
 
 /* 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 "hash.h"
 #include "jksql.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "tetDensity - density of tetraodon alignments vs. chromosomes\n"
   "usage:\n"
   "   tetDensity database\n");
 }
 
 char *chromNames[] =
     {
     "chr1",
     "chr2",
     "chr3",
     "chr4",
     "chr5",
     "chr6",
     "chr7",
     "chr8",
     "chr9",
     "chr10",
     "chr11",
     "chr12",
     "chr13",
     "chr14",
     "chr15",
     "chr16",
     "chr17",
     "chr18",
     "chr19",
     "chr20",
     "chr21",
     "chr22",
     "chrX",
     "chrY",
     };
 
 int tetCountInChrom(struct sqlConnection *conn, char *chrom)
 /* Number of tets in chromosome. */
 {
 char query[512];
 int tetCount = 0;
 int lastPos = -1000000;
 struct sqlResult *sr;
 char **row;
 int chromPos;
 
 sqlSafef(query, sizeof query, "select chromStart from %s_tet_waba", chrom);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     chromPos = sqlUnsigned(row[0]);
     if (chromPos - lastPos > 1000)
         ++tetCount;
     lastPos = chromPos;
     }
 sqlFreeResult(&sr);
 return tetCount;
 }
 
 int islandCountInChrom(struct sqlConnection *conn, char *chrom)
 /* Number of island in chromosome. */
 {
 char query[512];
 
 sqlSafef(query, sizeof query, "select count(*) from cpgIsland where chrom = '%s'", chrom);
 return sqlQuickNum(conn, query);
 }
 
 int knownCount(struct sqlConnection *conn, char *chrom)
 /* Number of island in chromosome. */
 {
 char query[512];
 
 sqlSafef(query, sizeof query, "select count(*) from genieKnown where chrom = '%s'", chrom);
 return sqlQuickNum(conn, query);
 }
 
 
 
 
 void chromTetDensity(struct sqlConnection *conn, char *chrom)
 /* Figure out density of tet alignments on one chromosome. */
 {
 char query[512];
 int chromSize;
 int tetCount = 0;
 int lastPos = -1000000;
 struct sqlResult *sr;
 char **row;
 int chromPos;
 
 sqlSafef(query, sizeof query, "select size from chromInfo where chrom = '%s'", chrom);
 chromSize = sqlQuickNum(conn, query);
 tetCount = tetCountInChrom(conn, chrom);
 printf("%5s %6.3f %6.3f %6.3f\n", chrom, 
     1000000.0*(double)tetCount/(double)chromSize/0.7712, 
     100000.0*(double)islandCountInChrom(conn, chrom)/(double)chromSize/0.3047,
     1000000*(double)knownCount(conn, chrom)/(double)chromSize/0.5597);
 }
 
 void tetDensity(char *database)
 /* tetDensity - density of tetraodon alignments vs. chromosomes. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 int i;
 
 printf("Chrom  tetrao cpgIsl known\n");
 for (i=0; i<ArraySize(chromNames); ++i)
     {
     chromTetDensity(conn, chromNames[i]);
     }
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc != 2)
     usage();
 tetDensity(argv[1]);
 return 0;
 }