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/snpOrtho.c src/hg/snp/snpLoad/snpOrtho.c
index 0f7dca5..c235cc4 100644
--- src/hg/snp/snpLoad/snpOrtho.c
+++ src/hg/snp/snpLoad/snpOrtho.c
@@ -1,130 +1,130 @@
 /* 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. */
 
 /* snpOrtho - read an ortho file with format:
    chrom chromStart chromEnd
    name (rsId) score strand allele */
 /* Read this into a hash */
 /* Then read (human) snp table serially. */
 /* Output:
    chrom chromStart chromEnd (human)
    name score strand
    refUCSC observed class locType weight
    orthoChrom orthoStart orthoEnd orthoScore orthoStrand orthoAllele */
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 
 
 struct hash *orthoHash = NULL;
 
 struct orthoSnp 
     {
     char *chrom;
     int start;
     int end;
     int score;
     char *strand;
     char *allele;
     };
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpOrtho - read ortho file; generate ortho table \n"
     "usage:\n"
     "    snpOrtho database snpTable orthoFile\n");
 }
 
 
 struct hash *getOrtho(char *inputFileName)
 /* put all orthoSnp objects in ret hash */
 {
 struct lineFile *lf = NULL;
 char *line;
 char *row[7];
 int elementCount;
 
 struct orthoSnp *orthoSnpInstance = NULL;
 struct hash *ret = newHash(16);
 int count = 0;
 
 verbose(1, "opening file %s\n", inputFileName);
 lf = lineFileOpen(inputFileName, TRUE);
 while (lineFileNext(lf, &line, NULL))
     {
     elementCount = chopString(line, "\t", row, ArraySize(row));
     if (elementCount != 7) continue;
     count++;
 
     AllocVar(orthoSnpInstance);
     orthoSnpInstance->chrom = cloneString(row[0]);
     orthoSnpInstance->start = sqlUnsigned(row[1]);
     orthoSnpInstance->end = sqlUnsigned(row[2]);
     orthoSnpInstance->score = sqlUnsigned(row[4]);
     orthoSnpInstance->strand = cloneString(row[5]);
     orthoSnpInstance->allele = cloneString(row[6]);
     hashAdd(ret, cloneString(row[3]), orthoSnpInstance);
     }
 lineFileClose(&lf);
 verbose(1, "%d rows in hash\n", count);
 return ret;
 }
 
 void writeResults(char *tableName)
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 
 struct hashEl *hel = NULL;
 struct orthoSnp *orthoData;
 
 char *snpId;
 
 FILE *outputFileHandle = mustOpen("snpOrtho.tab", "w");
 
 sqlSafef(query, sizeof(query), 
       "select chrom, chromStart, chromEnd, name, score, strand, refUCSC, observed, class, locType, weight from %s", 
       tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     snpId = cloneString(row[3]);
     hel = hashLookup(orthoHash, snpId);
     if (!hel) continue;
     orthoData = (struct orthoSnp *)hel->val;
     fprintf(outputFileHandle, "%s\t%s\t%s\t%s\t", row[0], row[1], row[2], snpId);
     fprintf(outputFileHandle, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t", row[4], row[5], row[6], row[7], row[8], row[9], row[10]);
     fprintf(outputFileHandle, "%s\t%d\t%d\t", orthoData->chrom, orthoData->start, orthoData->end);
     fprintf(outputFileHandle, "%d\t%s\t%s\n", orthoData->score, orthoData->strand, orthoData->allele);
     }
 
 carefulClose(&outputFileHandle);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 
 int main(int argc, char *argv[])
 /* generate snpOrtho table from snp ortho file */
 /* combine with snp table */
 {
 if (argc != 4)
     usage();
 
 hSetDb(argv[1]);
 if (!hTableExistsDb(argv[1], argv[2]))
     errAbort("can't get table %s\n", argv[2]);
 if (!fileExists(argv[3]))
     errAbort("can't find %s\n", argv[3]);
 
 orthoHash = getOrtho(argv[3]);
 writeResults(argv[2]);
 
 return 0;
 }