c6158bf203c8343c2562d8886f5bd9b1405b47dc
hiram
Tue Feb 19 13:56:24 2013 -0800
cosmic is changing its WEB site URL redmine 9386
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 9b2ee2f..aef95e9 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -9264,37 +9264,35 @@
mut_aa = row[ii];ii++;
tumour_site = row[ii];ii++;
mutated_samples = row[ii];ii++;
examined_samples = row[ii];ii++;
mut_freq = row[ii];ii++;
// chromosome name adjustment
if (sameString(chromosome, "23"))
chromosome = "X";
if (sameString(chromosome, "24"))
chromosome = "Y";
if (sameString(chromosome, "25"))
chromosome = "M";
chp = strstr(itemName, "COSM")+strlen("COSM");
- printf("COSMIC ID: %s", chp);
-
- printf(" (click here for more details at COSMIC site)\n", url, chp);
+ printf("COSMIC ID: %s (details at COSMIC site)", url, chp, chp);
// Embed URL to COSMIC site per COSMICT request.
printf("
Source: ");
- printf("%s\n", source);
+ printf("%s\n", source);
printf("
Gene Name: %s\n", gene_name);
printf("
Accession Number: %s\n", accession_number);
printf("
Genomic Position: chr%s:%s-%s", chromosome, grch37_start, grch37_stop);
printf("
Mutation Description: %s\n", mut_description);
printf("
Mutation Syntax CDS: %s\n", mut_syntax_cds);
printf("
Mutation Syntax AA: %s\n", mut_syntax_aa);
printf("
Mutation NT: %s\n", mut_nt);
printf("
Mutation AA: %s\n", mut_aa);
safef(query2, sizeof(query2),
"select count(tumour_site) from cosmicRaw where cosmic_mutation_id='%s'", itemName);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);