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/snp/snpLoad/snpSplitByChrom2.c src/hg/snp/snpLoad/snpSplitByChrom2.c
index 3f6eb21..3996bd5 100644
--- src/hg/snp/snpLoad/snpSplitByChrom2.c
+++ src/hg/snp/snpLoad/snpSplitByChrom2.c
@@ -1,155 +1,155 @@
 /* snpSplitByChrom2 - part of ortho pipeline. */
 
 /* 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 "hdb.h"
 
 
 static struct hash *chromHash = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpSplitByChrom2 - part of ortho pipeline\n"
     "usage:\n"
     "    snpSplitByChrom2 database table\n");
 }
 
 void loadChroms()
 /* hash chromNames, create file handles */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 FILE *f;
 char fileName[64];
 
 chromHash = newHash(0);
 sqlSafef(query, sizeof(query), "select chrom from chromInfo");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     safef(fileName, sizeof(fileName), "%s_snp125hg17ortho.tab", row[0]);
     f = mustOpen(fileName, "w");
     verbose(1, "chrom = %s\n", row[0]);
     hashAdd(chromHash, cloneString(row[0]), f);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 void getSnps(char *tableName)
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hashCookie cookie;
 struct hashEl *hel = NULL;
 
 sqlSafef(query, sizeof(query), 
     "select chrom, chromStart, chromEnd, name, strand from %s", 
     tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     hel = hashLookup(chromHash, row[0]);
     if (hel == NULL)
         verbose(1, "%s not found\n", row[0]);
     else
         fprintf(hel->val, "%s\t%s\t%s\t%s\t0\t%s\t%s\t%s\n", row[0], row[1], row[2], row[3], row[4], row[5], row[6]);
     }
 sqlFreeResult(&sr);
 cookie = hashFirst(chromHash);
 while ((hel = hashNext(&cookie)))
     fclose(hel->val);
 }
 
 void createTable(char *chromName)
 /* create a chrN_snp125hg17ortho table */
 {
 struct sqlConnection *conn = hAllocConn();
 char tableName[64];
 char *createString =
 "CREATE TABLE %s (\n"
 "    chrom varchar(15) not null default '',\n"
 "    chromStart int(10) not null default '0',\n"
 "    chromEnd int(10) not null default '0',\n"
 "    name varchar(15) not null default '',\n"
 "    score smallint(5) not null default '0',\n"
 "    strand enum('?','+','-') not null default '?'\n"
 ");\n";
 
 struct dyString *dy = newDyString(1024);
 
 safef(tableName, ArraySize(tableName), "%s_snp125hg17ortho", chromName);
 sqlDyStringPrintf(dy, createString, tableName);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 hFreeConn(&conn);
 }
 
 void loadDatabase(char *chromName)
 /* load one table into database */
 {
 FILE *f;
 struct sqlConnection *conn = hAllocConn();
 char tableName[64], fileName[64];
 
 safef(tableName, ArraySize(tableName), "%s_snp125hg17ortho", chromName);
 safef(fileName, ArraySize(fileName), "%s_snp125hg17ortho.tab", chromName);
 
 f = mustOpen(fileName, "r");
 hgLoadTabFile(conn, ".", tableName, &f);
 
 hFreeConn(&conn);
 }
 
 
 
 int main(int argc, char *argv[])
 {
 
 char *snpDb = NULL;
 char *snpTableName = NULL;
 struct hashCookie cookie;
 char *chromName = NULL;
 
 if (argc != 3)
     usage();
 
 snpDb = argv[1];
 hSetDb(snpDb);
 
 snpTableName = argv[2];
 
 /* check that tables exist */
 if (!hTableExists(snpTableName))
     errAbort("no %s table in %s\n", snpTableName, snpDb);
 if (!hTableExists("chromInfo"))
     errAbort("no chromInfo table in %s\n", snpDb);
 
 loadChroms();
 getSnps(snpTableName);
 
 verbose(1, "creating tables...\n");
 cookie = hashFirst(chromHash);
 while ((chromName = hashNextName(&cookie)) != NULL)
     createTable(chromName);
 
 verbose(1, "loading database...\n");
 cookie = hashFirst(chromHash);
 while ((chromName = hashNextName(&cookie)) != NULL)
     {
     verbose(1, "chrom = %s\n", chromName);
     loadDatabase(chromName);
     }
 
 return 0;
 }