5c1b49c05073cf23739c0b6998f869d33913c7af
galt
  Wed Sep 12 14:51:59 2012 -0700
adjust chromosome name from cosmicraw table for output
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 264cec7..4ad4c82 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -9258,30 +9258,38 @@
     accession_number    = row[ii];ii++;
     mut_description     = row[ii];ii++;
     mut_syntax_cds      = row[ii];ii++;
     mut_syntax_aa       = row[ii];ii++;
 
     chromosome          = row[ii];ii++;
     grch37_start        = row[ii];ii++;
     grch37_stop         = row[ii];ii++;
     mut_nt              = row[ii];ii++;
     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("<B>COSMIC ID:</B> %s", chp);
 
     printf(" (click <A HREF=\"%s&id=%s\" TARGET=_BLANK>here</A> for more details at COSMIC site)\n", url, chp);
 
     // Embed URL to COSMIC site per COSMICT request.
     printf("<BR><B>Source:</B> ");
     printf("<A HREF=\"http://www.sanger.ac.uk/cosmic/\" TARGET=_BLANK>%s</A>\n", source);
 
     printf("<BR><B>Gene Name:</B> %s\n", gene_name);
     printf("<BR><B>Accession Number:</B> %s\n", accession_number);
     printf("<BR><B>Genomic Position:</B> chr%s:%s-%s", chromosome, grch37_start, grch37_stop);
     printf("<BR><B>Mutation Description:</B> %s\n", mut_description);
     printf("<BR><B>Mutation Syntax CDS:</B> %s\n", mut_syntax_cds);
     printf("<BR><B>Mutation Syntax AA:</B> %s\n", mut_syntax_aa);