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/illuminaLookup2.c src/hg/snp/snpLoad/illuminaLookup2.c
index 8c4d563..12d2247 100644
--- src/hg/snp/snpLoad/illuminaLookup2.c
+++ src/hg/snp/snpLoad/illuminaLookup2.c
@@ -1,217 +1,217 @@
 /* illuminaLookup2 - validate illumina SNP arrays. */
 /* report if SNP missing */
 /* report unexpected position */
 /* check strand */
 /* check observed */
 /* report if class != single */
 /* report if locType != exact */
 
 /* 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"
 
 
 struct snpSubset 
     {
     char *chrom;
     int start;
     int end;
     char *strand;
     char *observed;
     char *class;
     char *locType;
     };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "illuminaLookup2 - just use rsId/chrom/pos from illumina\n"
     "usage:\n"
     "    illuminaLookup db illuminaPrelimTable snpTable exceptionTable \n");
 }
 
 
 struct hash *storeExceptions(char *tableName)
 /* store multiply-aligning SNPs */
 {
 struct hash *ret = NULL;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 
 verbose(1, "reading exceptions...\n");
 ret = newHash(0);
 sqlSafef(query, sizeof(query), "select name, exception from %s", tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if (!sameString(row[1], "MultipleAlignments")) continue;
     hashAdd(ret, cloneString(row[0]), NULL);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 struct hash *storeSnps(char *tableName, struct hash *exceptionHash)
 /* store subset data for SNPs in a hash */
 /* exclude SNPs that align multiple places */
 {
 struct hash *ret = NULL;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct snpSubset *subsetElement = NULL;
 struct hashEl *hel = NULL;
 
 verbose(1, "creating SNP hash...\n");
 ret = newHash(16);
 sqlSafef(query, sizeof(query), 
       "select name, chrom, chromStart, chromEnd, strand, observed, class, locType from %s", 
       tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     hel = hashLookup(exceptionHash, row[0]);
     if (hel != NULL)
 	continue;
     AllocVar(subsetElement);
     subsetElement->chrom = cloneString(row[1]);
     subsetElement->start = sqlUnsigned(row[2]);
     subsetElement->end = sqlUnsigned(row[3]);
     subsetElement->strand = cloneString(row[4]);
     subsetElement->observed = cloneString(row[5]);
     subsetElement->class = cloneString(row[6]);
     subsetElement->locType = cloneString(row[7]);
     hashAdd(ret, cloneString(row[0]), subsetElement);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 boolean biallelic(char *obs)
 {
 if (sameString(obs, "A/C")) return TRUE;
 if (sameString(obs, "A/G")) return TRUE;
 if (sameString(obs, "A/T")) return TRUE;
 if (sameString(obs, "C/G")) return TRUE;
 if (sameString(obs, "C/T")) return TRUE;
 if (sameString(obs, "G/T")) return TRUE;
 return FALSE;
 }
 
 
 void processSnps(struct hash *snpHash, char *illuminaTable)
 /* read illuminaTable */
 /* lookup details in snpHash */
 /* report and skip if SNP missing, class != single, locType != exact */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hashEl *hel = NULL;
 struct snpSubset *subsetElement = NULL;
 FILE *output = mustOpen("illuminaLookup.out", "w");
 FILE *errors = mustOpen("illuminaLookup.err", "w");
 int pos = 0;
 char *rsID = NULL;
 
 verbose(1, "process SNPs...\n");
 sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd, name from %s", illuminaTable);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     rsID = cloneString(row[3]);
     hel = hashLookup(snpHash, rsID);
     if (hel == NULL) 
         {
 	fprintf(errors, "%s not found\n", rsID);
 	continue;
 	}
     subsetElement = (struct snpSubset *)hel->val;
 
     if (!sameString(subsetElement->class, "single"))
         {
 	fprintf(errors, "unexpected class %s for snp %s\n", subsetElement->class, rsID);
 	continue;
 	}
 
     if (!sameString(subsetElement->locType, "exact"))
         {
 	fprintf(errors, "unexpected locType %s for snp %s\n", subsetElement->locType, rsID);
 	continue;
 	}
 
     if (!sameString(subsetElement->chrom, row[0]))
         {
 	fprintf(errors, "mismatch for snp %s (illumina = %s, dbSNP = %s)\n", rsID, row[0], subsetElement->chrom);
 	continue;
 	}
 
     pos = sqlUnsigned(row[1]);
     if (pos != subsetElement->start)
         {
         fprintf(errors, "mismatch position for snp %s (illumina = %d, dbSNP = %d)\n", rsID, pos, subsetElement->start);
 	continue;
 	}
 
     if (!biallelic(subsetElement->observed))
         {
         fprintf(errors, "snp %s not bi-alleleic\n", rsID);
 	continue;
 	}
 
     fprintf(output, "%s\t%s\t%s\t%s\t0\t%s\t%s\n", row[0], row[1], row[2], row[3], subsetElement->strand, subsetElement->observed);
 
     }
 
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 carefulClose(&errors);
 carefulClose(&output);
 }
 
 
 int main(int argc, char *argv[])
 /* load SNPs into hash */
 {
 char *snpDb = NULL;
 char *illuminaTableName = NULL;
 char *snpTableName = NULL;
 char *exceptionTableName = NULL;
 
 struct hash *snpHash = NULL;
 struct hash *exceptionHash = NULL;
 
 if (argc != 5)
     usage();
 
 snpDb = argv[1];
 illuminaTableName = argv[2];
 snpTableName = argv[3];
 exceptionTableName = argv[4];
 
 /* process args */
 hSetDb(snpDb);
 if (!hTableExists(illuminaTableName))
     errAbort("no %s table in %s\n", illuminaTableName, snpDb);
 if (!hTableExists(snpTableName))
     errAbort("no %s table in %s\n", snpTableName, snpDb);
 if (!hTableExists(exceptionTableName))
     errAbort("no %s table in %s\n", exceptionTableName, snpDb);
 
 exceptionHash = storeExceptions(exceptionTableName);
 snpHash = storeSnps(snpTableName, exceptionHash);
 processSnps(snpHash, illuminaTableName);
 
 return 0;
 }