+ /*
+ * VCF data may already contain the protein consequence
+ */
+ String hgvsp = sf.getValueAsString("CSQ", "HGVSp");
+ if (hgvsp != null)
+ {
+ int colonPos = hgvsp.indexOf(':');
+ if (colonPos >= 0)
+ {
+ String var = hgvsp.substring(colonPos + 1);
+ if (!vars.contains(var))
+ {
+ vars.add(var);
+ }
+ continue;
+ }
+ }
+
+ /*
+ * otherwise, compute codon and peptide variant
+ */
+ // todo avoid duplication of code in AlignmentUtils.buildDnaVariantsMap